LEC 11: Nucleic Acid
Human Genome Project
– An attempt to map all human genome
– Began in 1999
– working draft Feb 2001
– Finished 2003
– Collaboration of 20 labs in 6 countries
– Competition with Craig Ventnor, Celera
Genomic
Discoveries includes:
– 3.2 billion base pairs
– Only 30-40k genes
– Over 120k unique mRNA molecules
– Only 1-1.5 % of human DNA codes of
proteins.
 Each cell has 6ft of DNA = 1 inch
of exons to be transcribed
 Most of genome is “Junk DNA”
– Genes not evenly distributed
 Chromosome 19 packed with
Genes
 Large chromosomes 4 & 8 have
few transcribed genes
Nucleic Acids
– informational molecules
– the information to make all the functional
macromolecules of the cell (even DNA
itself) is preserved in DNA.
– elements of heredity; agents of genetic
information transfer.
Two Types:
• Deoxyribonucleic acid (DNA)
• Ribonucleic acid (RNA)
DNA
– repository of genetic information
in cells.
RNA
– serves in the expression of this
information through the processes
of transcription and translation
Exception:
some viruses have their genetic information
stored as RNA.
Roles of DNA
• DNA contains genes, the information
needed to synthesize functional proteins
and RNAs
• DNA contains segments that play a role
in regulation of gene expression (e.g.
promoters)
Roles of RNA
• Ribosomal RNAs (rRNAs) are
components of ribosomes, playing a role
in protein synthesis.
• Messenger RNAs (mRNAs) carry
genetic information from a gene to the
ribosome.
• Transfer RNAs (tRNAs) translate
information in mRNA into an amino acid
sequence.
• RNAs have other functions and can in
some cases perform catalysis.
Nucleic Acids
– polymers of nucleotides linked together
by phosphodiester bonds.
DNA
– is found in the nucleus (in eukaryotes)

– DNA is also found in mitochondria and

in chloroplasts, where it encodes some
of the proteins and RNAs unique to
these organelles.

Nucleotides and nucleic acids

Nucleotides Remove the phosphate group, and you have a

nucleoside.
– are the building blocks of nucleic acids.
– Nucleotides also play other important
roles in the cell.

Roles of nucleotides ATP is a nucleotide; energy currency

– Building blocks of nucleic acids (RNA,

DNA); analogous to amino acid role in
proteins

– Energy currency in cellular metabolism

(ATP: adenosine triphosphate)

– Allosteric effectors

– Structural components of many enzyme

cofactors (NAD: nicotinamide adenine
dinucleotide) Below is the general structure of a nucleotide.
The pentose sugar, the base, and the
Structure of nucleotides phosphate moieties all show variations among
nucleotides.
Nucleotides have three characteristic
components:

• phosphate group
• nitrogenous base (pyrimidine or purine)
• pentose sugar
 Ribose sugar Purine or Pyrimidine base

– Nucleotide bases in nucleic acids are

Ribose pyrimidines or purines.

– Ribose (b-D-furanose) is a pentose

sugar (5-membered ring).

– Note numbering of the carbons. In a

nucleotide, "prime" is used (to
differentiate from base numbering).

Major bases in nucleic acids

– An important derivative of ribose is 2'-
deoxyribose, or just deoxyribose, in The bases are abbreviated by their first letters
which the 2' OH is replaced with H. (A, G, C, T, U).

– Deoxyribose is in DNA
(deoxyribonucleic acid)
– Ribose is in RNA (ribonucleic acid).
– The sugar prefers different puckers in
DNA (C-2' endo) and RNA (C-3' endo).
The purines (A, G) occur in both RNA and DNA
Among the pyrimidines:
• C occurs in both RNA and DNA
• But T occurs in DNA.
• U occurs in RNA.
 Phosphate

Variation in phosphate group
2'-deoxyribose sugar
Adenosine 3', 5'-cyclic monophosphate
(cyclic AMP, or cAMP)
– is an important regulatory nucleotide.
Another variation - multiple phosphates (like
ATP).
Deoxyribonucleotides
– with a base (here, a purine, adenine or
guanine)
– attached to the C-1' position is a
deoxyribonucleoside (here
deoxyadenosine and deoxyguanosine).
– Phosphorylate the 5' position and you
have a nucleotide(here, deoxyadenylate
or deoxyguanylate)
– Deoxyribonucleotides are abbreviated
(for example) A, or dA (deoxyA), or
dAMP (deoxyadenosine
monophosphate)

Nucleotides in nucleic acids

Bases
– attach to the C-1' of ribose or The major deoxyribonucleotides
deoxyribose

Pyrimidines
– attach to the pentose via the N-1
position of the pyrimidine ring

Purines
– attach through the N-9 position

Some minor bases may have different

attachments.

Ribonucleotides
Ribose sugar
– with a base (here, a pyrimidine, uracil or
cytosine) attached to the ribose C-1'
position is a ribonucleoside (here,
uridine or cytidine).
– Phosphorylate the 5' position and you
have a ribonucleotide (uridylate or
cytidylate)
The major ribonucleotides
Nucleotide nomenclature
Nucleic Acid
Levels of structure
• 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
1. 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)
Nucleotide monomers
– can be linked together via a
phosphodiester linkage.
– formed between the 3' -OH of a
nucleotide.
– and the phosphate of the next
nucleotide.
– Two ends of the resulting poly- or
oligonucleotide are defined:
– The 5' end lacks a nucleotide at the 5'
position,
– and the 3' end lacks a nucleotide at the
3' end position.
 handed manner about the same axis. Structure
based on X-Ray crystallography
Sugar-phosphate backbone

– The polynucleotide or nucleic acid

backbone thus consists of alternating
phosphate and pentose residues.

– The bases are analogous to side chains

of amino acids; they vary without
changing the covalent backbone
structure.

– Sequence is written from the 5' to 3' DNA strands

end: 5'-ATGCTAGC-3'
– The antiparallel strands
of DNA are not identical
– Note that the backbone is polyanionic.
but are complementary.
Phosphate groups pKa ~ 0.
– This means that they are
positioned to align
complementary base
pairs: C with G, and A
with T.

– So, you can predict the

Compare polynucleotides and polypeptides sequence of one strand
given the sequence of its
– As in proteins, the sequence of side complement.
chains (bases in nucleic acids) plays an
important role in function. – Useful for information
storage and transfer!
– Nucleic acid structure depends on the – Note sequence conventionally
sequence of bases and on the type of is given from the 5' to 3' end.
ribose sugar (ribose, or 2'-deoxyribose).
Interstrand H-bonding
– Hydrogen bonding interactions are between DNA bases
especially important in nucleic acids.

2. DNA - 2° Structure

– the ordered arrangement of nucleic acid

strands.
– the double helix model of DNA
2°structure 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-

DNA structure determination
– Chargaff’s results of DNA studies
(1940s):
– The four bases found in DNA do not
occur in equimolar amounts; the relative
amounts of each vary from species to
species.
– There are 10.5 base pairs, or 36 Å, per
turn of the helix.
– Alternating deoxyribose and
phosphate groups on the backbone
form the outside of the helix.
– The planar purine and pyrimidine
bases of both strands are stacked inside
the helix.

– A=T; G=C

– Number of pyrimidine residues always

equals the number of purines residues.

Chargaff’s rule: [A]=[T]; [C]=[G]; [pyrimidines]

= [purines]

DNA structure determination – The furanose ring usually is puckered

Franklin collected x-ray diffraction data (early
1950s) that indicated 2 periodicities for DNA:
3.4 Å and 34 Å.
Watson and Crick proposed a 3-D model
accounting for the data.
in a C-2' endo conformation in DNA.
– The offset of the relationship of the base
pairs to the strands gives a major and a
minor groove.
– In B-form DNA (most common) the
depths of the major and minor grooves
are similar to each other.

Base stacking in DNA

– C-G (red) and A-T (blue) base pairs are

isosteric (same shape and size),
allowing stacking along a helical axis for
any sequence.

DNA structure – Base pairs stack inside the helix.

– DNA consists of two helical chains
wound around the same axis in a right-
handed fashion aligned in an antiparallel
fashion.
 • B form - The most common
conformation for DNA.
Denaturation
• A form - is favored in conditions of low
water (high salt concentration)
• Z form - narrow, deep minor groove.
Major groove hardly existent.
Dehydration of the DNA molecule and
methylation of cytosine residues in alternating
CG sequences can result in the shift from the B
to Z conformation.
Denaturation of DNA
– 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)

3. DNA - 3° 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
Prokaryotic DNA
– is circular and it can form supercoils.
Topological changes induced by supercoiling
accommodated by histone-protein component
of chromatin.
Structure of chromatin
– Each “Bead” is a nucleosome
– Nucleosome consists of: DNA wrapped
around histone core.

Double helix can be considered to a 2-

stranded, right-handed coiled rope. Hence, it
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 Note: simple life forms such as viruses or
• H4 bacteria usually contain a single DNA
(or “chromosome”)
Chromatin
– DNA molecules wound around particles E. coli chromosome
of histones in a beadlike structure
– has a molecular mass of 2.9 x 10 9 Da
and contains more than 9 million
nucleotides.
– Eukaryotic cells have many
chromosomes, and DNA is usually
found principally in two copies in the
diploid chromosomes of the nucleus
RNA molecules are classified according to
their structure and function
tRNAs (Transfer RNA)
– Synthesized also by transcription of
DNA , but unlike mRNA molecules, are
not subsequently translated to form
proteins.
– Transfer RNAs (tRNAs) translate
information in mRNA into an amino acid
sequence.
– Carrier of amino acids to the site of
synthesis of proteins (ribosomes)
– Is a small RNA that has a very specific
secondary and tertiary structure such
that it can bind an amino acid elements
of a protein to the appropriate place as
coded for by the mRNA.
• Dihydrouridine
• Inosine
• Thiouridine
• Pseudouridine
• Hypermethylated Purines
= unusual bases in tRNA
RNA displays interesting tertiary structure
Ribosomal RNA
Ribosomal RNAs (rRNAs) are components of
ribosomes.
Ribosomes
– composed of two subunits of two
different sizes; each subunit is a
supramolecular assembly of proteins
(35%) and RNA (65%).
– particles characterized by sedimentation
coefficients, expressed in Svedberg
units (S)
mRNAs
Messenger RNAAs
– transcribed copies of the protein-coding
genetic units of DNA.
– Synthesized during transcription.
– Prokaryotic mRNAs have from 75 to
3,000 nucleotides.
 – Constitutes about 2% of the total
prokaryotic RNA.
– Delivers genetic information from
nucleus to the cytoplasm.
– RNA nucleotides are complementary to
DNA nucleotides (exception: no T in
RNA; replaced with U)

In prokaryotes, a single mRNA may contain the

information for the synthesis of several
polypeptide chains within its nucleotide
sequence.

In contrast, eukaryotic mRNAs encode only

one polypeptide but are more complex in that
they are synthesized in the nucleus in the form
of much larger precursor molecules known as
heterogeneous nuclear RNA or hnRNA
(contain non-coding sequences or intervening
sequences)

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.