Nucleic acids
Nucleic Acids
Nucleic acids are polymers of subunits called nucleotides
A nucleotide is composed of:
A phosphate group
A pentose (five carbon) sugar
Deoxyribose in DNA
Ribose in RNA
A nitrogenous base
Guanine
Cytosine
Adenine
Thymine (DNA only)
Uracil (RNA only)
Nucleotides
The carbon position in the sugar is a key factor in the structure of a
nucleotide. The phosphate bonds to the fifth carbon (referred to as the
5 prime position, or 5’). One of the five nitrogen bases bonds to the
first carbon (referred to as the 1 prime position, or 1’).
In diagrams of nucleotides use circles, pentagons and rectangles to
represent relative positions of phosphates, pentose sugars and bases.
Purines and Pyrimidines
The nitrogenous bases have two basic structures - either purines or
pyrimidines
The purines have a double ring structure (adenine and guanine)
The pyrimidines have a single ring structure (cytosine, thymine and uracil)
Purines and Pyrimidines
Formation of a Polynucleotide
Nucleotides are linked to form a single
polynucleotide strand via condensation reactions
(water is produced)
The 5’- phosphate group of one nucleotide
attaches to the sugar of another nucleotide at
the 3’- hydroxyl group
The bond that is formed between the two
nucleotides is a covalent phosphodiester bond
(shown as red line to the right)
The sugars and phosphates are
bonded by covalent bonds,
making a very strong and rigid
‘back bone’
DNA Structure
Purines and pyrimidines are attracted to each
other by hydrogen bonds to form base pairs (BP)
These hydrogen bonds cause two nucleic acid
chains to join to form a double stranded molecule
The DNA strands are complementary due to the
base pair rule:
Adenine always bonds to Thymine (A -- T)
Cytosine always bonds to Guanine (C -- G)
Note: two hydrogen bonds form between A/T and three
hydrogen bonds form between C/G
Directions
In order for two sets of nitrogenous bases to
pair, the two DNA strands must run in
antiparallel directions
The pentose sugars ‘point’ in opposite directions
The direction is determined by the carbons in
the deoxyribose ring
The strand with a free third carbon on the sugar is
called the 3’ end
The strand with a phosphate bonded to the fifth
carbon on the sugar is called the 5’ end
The Double Helix
The pairing of a double-ringed purine to a single-
ringed pyrimidine ensures the stability of the DNA
double helix and ensures the backbones remain
separated by a constant width throughout the DNA
molecule
The sugar phosphate backbone is hydrophilic, so it
orients itself outward toward the solvent, while the
relatively hydrophobic bases are towards the centre
The double-stranded molecule then twists due to
forces between the bases of adjacent nucleotides in
order to adopt the most stable energy configuration
Roughly 10 – 15 base pairs per rotation
The helix forms major and minor grooves
DNA Structure
RNA
RNA differs from DNA, the sugar in the backbone
is ribose and thymine is replaced by uracil
RNA is usually single-stranded but can form loops
via complementary base pairing
The three main types are messenger RNA, transfer
RNA and ribosomal RNA
DNA and RNA Comparison
DNA and RNA Comparison
DNA RNA
Structure Typically double stranded
Long chain of nucleotides
Typically single stranded
Much shorter chain of nucleotides
Sugar and
Bases
Sugar – Deoxyribose
Bases – Guanine, Cytosine, Adenine
and Thymine (G, C, A, T)
Sugar – Ribose
Bases – Thymine is replaced with Uracil (G,
C, A, U)
Role Long term storage of genetic
information
Transfer of the genetic code from the DNA
needed for the creation of proteins
• Messenger RNA (mRNA)
• Transfer RNA (tRNA)
• Ribosomal RNA (rRNA)
Unlocking DNA - Discovery and Experimentation
In 1869, Friedrich Miescher discovered DNA in leukocytes (white blood cells )
in pus from bandages
He knew that it was found in the nuclei of cells, so he called it nuclein
He knew that it didn’t dissolve in organic solvents (not a lipid), it wasn’t broken down by
proteases (not a protein), and contained carbon, hydrogen, oxygen, nitrogen phosphorus
In 1878, Albrecht Kossel isolated the bases
In 1919, Phoebus Levene worked out that each nucleotide consisted of a sugar
(deoxyribose), phosphate and base
He proposed that DNA was a short chain of four nucleotides in a set pattern (the
tetranucleotide hypothesis)
He thought that this molecule was far too simple to be the genetic code
Chargaff
In 1949 Erwin Chargaff used paper chromatography
and UV spectrophotometry to demonstrate that the
frequency of the four bases was not equal, falsifying
the tetranucleotide hypothesis
He repeated the experiment with multiple different
species and found that specific purines and
pyrimidines occurred in equal ratios, suggesting the
possibility that these bases occur in pairs
% of adenine = % of thymine
% of cytosine = % of guanine
Different species had different base compositions but
the same ratios of A/T and C/G, supporting the
proposition that DNA was the genetic material
Hershey-Chase
In 1952, Alfred Hershey and Martha Chase conducted a series of experiments to prove
that DNA was the genetic material
Viruses grown in radioactive
sulfur (
35S) had radiolabelled
proteins (sulfur is present in
proteins but not DNA)
Viruses grown in radioactive
phosphorus (32P) had
radiolabeled DNA (phosphorus is
present in DNA but not proteins)
The bacterial was found to be
radioactive when infected by
the 32P–viruses (DNA) but not
the 35S–viruses (protein)
Franklin, Watson and Crick
In 1952, Rosalind Franklin showed that DNA was a
helix using X-ray crystallography
In 1953, James Watson and Frances Crick used
Chargaff’s Ratio and Franklin’s X-ray data to build
models of the structure of DNA and demonstrate the
double helix
Review
Complete the DNA
structure diagram on the
worksheet to include the
following information:
Sugar phosphate backbone
Complementary base pairs
Correct bonding of all
components
Antiparallel directionality
One individual nucleotide
Review
Chromosomes and Chromatin
Chromosomes are threadlike
structures made of protein and a
single molecule of DNA that serve to
carry the genomic information
Chromatin is a combination of DNA,
histone protein, and other proteins
that makes up chromosomes
Chromosomes are found inside the
nuclear envelope of eukaryotic cells
Nucleosomes
A nucleosome consists of a molecule of DNA wrapped around a core of
eight histone proteins (an octamer)
The negatively charged DNA associates with the positively charged amino
acids on the surface of the histone proteins
The DNA is coiled around the histone octamer in a manner that resembles
thread being wrapped around a spool
Individual nucleosomes are together linked by an additional histone protein (H1
histone) attached to linker DNA
The nucleosomes are then folded into increasingly more complicated structures,
eventually forming chromatin
Nucleosomes
Nucleosomes help to supercoil the DNA,
which helps package DNA into a smaller
volume to fit in the nucleus, protects the
DNA from damage, and regulates the
level of transcriptional activity
The histone proteins have N-terminal tails
which extrude outwards from the nucleosome
– these tails determine how tightly the DNA is
packaged
Chromatin
The functions of chromatin are:
To package DNA into a smaller volume to fit in the cell and nucleus
To strengthen the DNA to allow mitosis and meiosis to occur
To control gene expression and DNA replication
Heterochromatin (condensed) is tightly packed and often indicates the
DNA region is transcriptionally inactive
Euchromatin (extended) is high in gene concentration and often indicates
higher amounts of transcription is occurring
DNA Packaging
Heterochromatin (condensed) is tightly packed and often
indicates the DNA region is transcriptionally inactive
Euchromatin (extended) is high in gene concentration and
often indicates higher amounts of transcription is occurring
The H1 histone helps the chromatin fibre form looped
domains
The looped domains are attached to a scaffold non-
histone protein
The looped domains themselves fold repeatedly
Repeated folding produces the condensed chromosome
that is visible during cell division