NUCLIC ACID STRUCTURE AND
FUNCTION
• Topics to be covered are:
Central Dogma of Biology
The
potential
of
life
sciences
biotechnology application
Nuclic acid(DNA and RNA) Structure
and
Central Dogma of Biology
• Proposed by F. Crick in 1956
• It is the genetic information flow from the
nucleotide sequence of genes to the structure
of proteins.
• The flow of information is therefore composed
of two successive steps, transcription and
translation.
• DNA → DNA → RNA → Protein
• replication → transcription → translation
Pathway of the central dogma in a cell
Cont….
• (i) DNA is the template for its self-replication
(requires proteins)
• (ii) RNA synthesis (transcription) is directed
by a DNA template
• (iii) Protein synthesis (translation) is directed
by an RNA template and is performed by
ribosomes with the help of aminoacylatedtransfer RNAs (aa-tRNAs)
Cont….
• Flow of genetic information is still valid: but
Proteins never serve as a template for RNA
synthesis (i.e. the complete reversal of the
proposed genetic flow is impossible).
Cont….
• However, RNA can sometimes serve as a
template for the synthesis of complementary
DNA sequences.
• RNA genomes from Retroviruses are
converted in a DNA copy (by the enzyme
reverse transcriptase) that is used as a
replicative form
The potential of life sciences and
biotechnology
• Enabling technology (like IT): wide range of
purposes for private and public benefits
– Health care
– Agro-food
– Non-food uses of crops
– Environment
Health care
• To find cures for the diseases
• To replace existing cures becoming less
effective (e.g., antibiotics).
• To provide personalized and preventive
medicine based on genetic predisposition,
targeted screening, diagnosis and innovative
drug treatments (pharmacogenomics)
• To offer replacement tissues and organs (stem
cell research, xenotransplantation)
Agro-food
• Disease prevention
• Reduced health risks
• Functional food
• Reduced use of pesticides, fertilizers and drugs
• Fight hunger and malnutrition
Non-food uses of crops
• Complex molecules for the manufacturing,
energy and pharmaceutical industries
• Biodegradable plastics, biomass energy, new
polymers, etc.
Environment
• Bioremediation of polluted air, soil, water and
waste
• Cleaner industrial products and processes (e.g.
enzymes or biocatalysis)
Fields of application
Primary production through agriculture, forestry,
fishing: ‘green’
-Health and pharmaceutical sector: ‘red’
-Industry/environment: ‘white
THE NUCLEIC ACIDS
Nucleic acids are the third class of biopolymers
(polysaccharides and proteins being the others)
• Two major classes of nucleic acids:DNA and RNA
• Deoxyribonucleic acid (DNA):
• Carrier of genetic information
• DNA from a single human cell extends in a single
thread for almost 2 meters long!!!
• It contains information equal to some 600,000 printed
pages of 500 words each!!!
(a library of about 1,000 books)
Ribonucleic
acid
(RNA):
an intermediate in the expression of genetic
information
and
other
diverse
roles.
HSTORICAL BACKGROUND
• Friedrich Miescher in 1869
• Isolated what he called nuclein from the nuclei
of pus cells
• Nuclein was shown to have acidic properties,
hence it is called nucleic acid
Cont…
1944: Avery, MacLeod & McCarty - Strong evidence
that DNA is genetic material
1950: Chargaff - careful analysis of DNA from a wide
variety of organisms.
Content of A,T, C & G varied widely according
to the organism, however: A=T and C=G (Chargaff’
Rule)
1953: Watson & Crick - structure of DNA (1962 Nobel
Prize with M. Wilkens)
Erwin Chargaff’s Data (1950-51)
The distribution of nucleic acids in the
eukaryotic and Prokaryotes cell
• In eukaryotes DNA is found in the nucleus
with small amounts in mitochondria and
chloroplasts
• In Prokaryotes (Bacteria and Archaea) have no
nucleus.
• Appears as a granular structure associated with
the membrane, the nucleoid.
• RNA is found throughout the cell
DNA and its structure
• 1o Structure - Linear array of nucleotides
• 2o Structure – double helix
• 3o Structure - Super-coiling, stem-loop
formation
• 4o Structure – Packaging into chromatin
Determination of the DNA 1o Structure
(DNA Sequencing)
• Can determine the sequence of DNA base
pairs in any DNA molecule
• Chain-termination method developed by
Sanger
• Involves in vitro replication of target DNA
•
•
> ETH/31054/2015_pM13F
CCTACCTCCTTCAACTACGGTGCCATCAAGGCCACTAGGGTGGTTGAACTGCTTTACCGCATGAA
GAGAGCTGAGACATACTGTCCTCGGCCTCTTTTAGCCATCCAGCCAAGTGAAGCCAGACACAAA
CAGAAGATAGTGGCGCCTGTAAAACAGCTTCTGAACTTTGACTTACTCAAGTTGGCAGGAGACG
TTGAGTCCAACCCTGGGCCCTTC
DNA Secondary structure
(X-ray christalpgraphy)
• DNA is double stranded with antiparallel
strands
• Three different helical forms (A, B and Z
DNA.
Comparison of A, B, Z DNA
• A: right-handed, short and broad, 2.3 A, 11 bp
per turn
• B: right-handed, longer, thinner, 3.32 A, 10 bp
per turn
• Z: left-handed, longest, thinnest, 3.8 A, 12 bp
per turn
A- form DNA
• A-form DNA is a less hydrated form of dsDNA.
• Is a regular, right-handed helix
• Double stranded RNA and DNA-RNA hybrids and of
double-stranded DNA stretches in some DNA-protein
complexes.
• A-DNA is shorter and larger than B-form DNA
• The bases are not lying flat as in B-form DNA, but
they are slightly tilted(+19°)
Cont…
• It is more compact and is underwound(11
bp/turn; rise = 2.3 Å).
• The major groove of A-form DNA is narrower
and deeper
• The minor groove is superficial, flat and broad.
• The sugars are in the C3'-endo configuration
B-form DNA
• In vivo most of the DNA is supposed to exist
in the B-form.
• Regular,right-handed helix (diameter of 20 Å)
• It has on average 10.5 bp per turn and a rise of
3.32 Å .
• The pentose C2' is in the endo-configuration
and the bases in the anti conformation.
• The bases are lying approximately flat and
perpendicular with respect to the helical axis
(only tilted by -1.2°)
Cont…
• The minor groove is narrower and very deep.
• The major groove in B-form DNA is no longer
a groove but a convex surface.
Z-form DNA
• Z-form DNA is the only left-handed form of
DNA
• It has about 12 bp/turn and a rise of 3.8 Å/bp
• Z-DNA is skinny
• The plane of the base is slightly tilted with
respect to the helical axix (-9°)
• Its name indicates the zig-zag structure of the
backbone
Cont…
• The molecular basis is the synconformation
(rotation around the glycosidic bond) of the
guanines
• C3'-endo conformation of the sugar moieties
(C2’-endo and anti-configuration for the
cytosine residues).
The bond joining the 1′-carbon of the deoxyribose
sugar to the heterocyclic base is the N-glycosidic
bond.
Rotation
about
this
bond
gives
rise
to syn and anti conformations.
The syn conformation is fully allowed but the anti one
is partly allowed
DNA 3o Structure
 Triple-stranded DNA
• Is an important intermediate, generated by the
action of the RecA protein in the process of
homologous DNA recombination.
 The cruciform structure
• Complementary pairing of inverted repeat
sequences in a single strand.
• Typical intermediates in the resolution process
of
recombining
molecules
(Holliday
junctions).
•Cruciforms occur in palindromic
regions of DNA
•Can form intrachain base pairing
DNA 4o Structure
• In chromosomes, DNA is tightly associated with
proteins .
• One cell Human DNA’s total length is ~2 meters!
• This must be packaged into a nucleus that is about 5
micrometers in diameter
• This represents a compression of more than 100,000!
• It is made possible by wrapping the DNA around
protein spools called nucleosomes and then packing
these in helical filaments
•4 major histone (H2A, H2B,
H3, H4) proteins for octomer
•200 base pair long DNA
strand winds around the
octomer
•146 base pair DNA “spacer
separates individual
nucleosomes
•H1 protein involved in
higher-order chromatin
structure.
•With out H1, Chromatin
looks like beads on string
Solenoid Structure of Chromatin
NUCLEIC ACID STRUCTURE
• Nucleic acids are polynucleotides
• Their building blocks are monomeric units called
nucleotides
• Nucleotides are made up of three structural subunits
•
1. Sugar: ribose in RNA, 2-deoxyribose in DNA
•
2. Heterocyclic base(A,G(pu),C,T(Py))
•
3. Phosphate
NUCLEOTIDE STRUCTURE
PHOSPATE
SUGAR
BASE
Ribose or
Deoxyribose
PURINES PYRIMIDINES
Adenine
(A)
Guanine(
G)
NUCLEOTIDE
Cytocine (C)
Thymine (T)
Uracil (U)
Nucleoside, nucleotides and nucleic acids
phosphate
sugar
phosphate
phosphate
sugar
base
base
sugar
base
sugar
base
phosphate
nucleoside
nucleotides
sugar
base
nucleic acids
The chemical linkage between monomer units in nucleic acids
is a phosphodiester
Sugar : Ribose is a pentose
C5
O
C1
C4
C3
C2
It can be of :
DEOXYRIBOSE
RIBOSE
CH2OH
O
C
H
H
H
C
OH
OH
CH2OH
C
C
H
H
OH
O
C
H
H
C
C
C
OH
OH
H
H
P
THE SUGAR-PHOSPHATE
BACKBONE
• The nucleotides are all
orientated in the same
direction
• The phosphate group joins the
3rd Carbon of one sugar to the
5th Carbon of the next in line.
P
P
P
P
P
P
G
ADDING IN THE BASES
P
C
• The
bases
are
attached to the 1st
Carbon
• Their
order
is
important
It determines the
genetic information of
the molecule
P
C
P
A
P
T
P
T
Hydrogen bonds
P
G
C
P
Phosphodiester bond
DNA is Made of Two
Strands of Polynucleotide
Glycocidic bond
P
C
P
P
C
C1 =N9(purine)
C1=N1(pyrimidine)
G
G
P
P
A
T
P
P
T
A
P
Glycocidic bond
P
T
A
P
DNA is Made of Two Strands of Polynucleotide
• The sister strands of the DNA molecule run in opposite
directions (antiparallel)
• They are joined by the bases
• Each base is paired with a specific partner:
A is always paired with T
G is always paired with C
Purine with Pyrimidine
• This the sister strands are complementary but not
identical
• The bases are joined by hydrogen bonds, individually
weak but collectively strong
© 2007 Paul Billiet ODWS
Cont…
7
NH2
6
N
5
N
H
4
N
8
9
1
N
2
N
H
N3
N
H
N
NH2
6
3
2
N1
pyrimidine
H3C
N
N
H
O
cytosine (C)
DNA/RNA
NH
N
NH2
guanine (G)
DNA/RNA
O
4
N
N
N
adenine (A)
DNA/RNA
purine
5
O
O
NH
N
H
O
thymine (T)
DNA
NH
N
H
O
uracil (U)
RNA
Pyrimidines and Purines. The heterocyclic base; there
are five common bases for nucleic acids
Note that G, T and U exist in the keto form (and not the enol
form found in phenols)
7
N
NH2
6
5
N
8
9
N
H
4
1
N
2
N
H
N3
N
H
N
NH2
N3
2
N1
pyrimidine
H3C
N
N
H
O
cytosine (C)
DNA/RNA
NH
N
NH2
guanine (G)
DNA/RNA
O
4
6
N
N
adenine (A)
DNA/RNA
purine
5
O
O
NH
N
H
O
thymine (T)
DNA
NH
N
H
O
uracil (U)
RNA
Nucleosides. N-Glycosides of a purine or pyrimidine
heterocyclic base and a carbohydrate. The C-N bond involves
the anomeric carbon of the carbohydrate. The carbohydrates for
nucleic acids are D-ribose and 2-deoxy-D-ribose
45
Watson & Crick Base pairing
7
N
NH2
6
5
N
8
9
N
H
4
1
N
2
N
H
N3
N
H
N
NH2
6
2
N1
pyrimidine
Watson-Crick base pairing requires
that the bases be in their preferred
tautomeric states, that is with keto
(C=O) and exocyclic amino (NH2)
groups, not the enol (C-OH) and
imino(N-H) forms.
H3C
N
N
H
O
cytosine (C)
DNA/RNA
NH
N
NH2
guanine (G)
DNA/RNA
O
4
N3
N
N
adenine (A)
DNA/RNA
purine
5
O
O
NH
N
H
O
thymine (T)
DNA
NH
N
H
O
uracil (U)
RNA
The Double Helix (1953)
© Dr Kalju Kahn USBC Chemistry and Biochemistry
Public Domain image
Why Triple bond in C=G and double
bond in A=T base pairing ?
Hydrogen bridges form between an electronegative group
and an electropositive hydrogen atom.
The double bonded O='s from cytosine and guanine are
very electronegative, because the oxygen nucleus pulls
strongly to the shared electron pairs.
In the central ring, a likewise, but weaker phenomenon
takes place.
The cytosine nitrogen atom pulls electrons from the shared
electron pairs with surrounding C atoms and, hence,
becomes electronegative too.
It attracts the positively charged H atom of guanine, hence
creating a hydrogen bond.
Why a helix?
• DNA inside a cell is surrounded by water.
• Sugar and phosphate are hydrophilic but the
bases are hydrophobic.
• Therefore the bases will try to escape from the
water.
• This will make the DNA to have helical
structure.
Why is 2'-Deoxyribose the Sugar Moiety in
DNA?
• Perhydroxylated sugars ( glucose and ribose)
formed in nature as products of the reductive
condensation of carbon dioxide and an
additional biological reduction steps.
• This is because the extra hydroxyl group in
ribose is:
• Bulky(interfere double helix structure and
prevent efficient packing)
• Reactive 2'-hydroxyl(for lifetime stability of
an organism)
Why triple hydrogen bond between G>C and A>T
Triple bond
• Hydrogen bonds form between a hydrogen
bond donor and a hydrogen bond acceptor.
• If we speak for the nucleic acid bases, here
are the donors and acceptors
• See, between Cytosin and Guanine, we see 3
pairs of acceptor-donor. Hydrogen of NH2
functions as donor, whereas oxygen atom
right across functions as acceptor.
Double bond
• Between Thymine and Adenine, only 2
hydrogen bonds can form as the distance
between a 2 donors and 2 acceptors allows
them to.
• Remember that, the distance whence a
hydrogen bond can form is roughly around 2–
4 Angström.