Transcript lec1 Introduction to nucleic acids

INTRODUCTION TO
NUCLEIC ACIDS
Friedrich Miescher in 1869
• isolated what he called nuclein from the nuclei
of pus cells
• Nuclein was shown to have acidic properties,
hence it became called nucleic acid
Two types of nucleic acid are
found
• Deoxyribonucleic acid (DNA)
• Ribonucleic acid (RNA)
The distribution of nucleic acids
in the eukaryotic cell
• DNA is found in the nucleus
with small amounts in mitochondria
• RNA is found throughout the cell
DNA as genetic material
1.
2.
3.
Present in all cells and virtually restricted to the nucleus
The amount of DNA in somatic cells (body cells) of any given
species is constant (like the number of chromosomes)
The DNA content of gametes (sex cells) is half that of somatic
cells.
In cases of polyploidy (multiple sets of chromosomes) the DNA
content increases by a proportional factor
Deoxyribose Nucleic Acid.
DNA contains all the information necessary
for all living organisms to grow and live.
(i.e. a blueprint for life).
NUCLEIC ACID STRUCTURE
• Nucleic acids are polynucleotides
• Their building blocks are nucleotides
NUCLEOTIDE STRUCTURE
PHOSPATE
BASE
SUGAR
Ribose or
Deoxyribose
PURINES
PYRIMIDINES
Adenine (A) Cytocine (C)
Guanine(G) Thymine (T)
Uracil (U)
NUCLEOTIDE
Ribose is a pentose
C5
O
C1
C4
C3
C2
Spot the difference
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
5
The bases
The most common organic bases are
Adenine
(A)
Thymine
(T)
Cytosine
(C)
Guanine
(G)
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Nucleotides
The deoxyribose,
the phosphate
and one of the bases
Combine to form a nucleotide
PO4
adenine
deoxyribose
Nitrogenous bases
Pyrimidines
cytosine (C) thymine (T) uracil (U)
Have One ring;
Purines
Have two rings
adenine (A) guanine (G)
Complementarity of bases
T (U) and A, C and G.
Pyrimidines and Purines
• Pyrimidine and purine are the names of the
parent compounds of two types of nitrogencontaining heterocyclic aromatic
compounds.
6
N1
5
4
N
3
Pyrimidine
2
7
N
5
9
N
H
4
8
6
N1
N
3
Purine
2
• The nitrogen containing bases are the only
difference in the four nucleotides.
Nucleotide & Nucleoside
Basic building block of nucleic acid
It consist of
A sugar (ribose or deoxyribose)
A nitrogenous base (purine &
pyrimidine rings)
A phosphate
Nucleosides= Base + Sugar
They glycosylamines consisting of a nucleobase bound to
a ribose or deoxyribose sugar via a beta-glycosidic
linkage.
Structures of Nucleosides
Structures of Nucleotides
When phosphate group is added to the above nucleosides then the
nucleotide is formed.
When a single phosphate group is added to the nucleoside then
it is called as mononucleotide.
The bond between pentose and base is b-N-glycosidic bond. N9 of
purine ring binds with C1 of pentose sugar. In pyrimidines the bond
is in between N1 of pyrimidine and C1 of pentose.
When a phosphate group is attached at 5' position of a sugar then it
is written as Adenosine 5'-monophosphate (AMP).
The nucleotides are abbreviated by three capital letters, preceded by
d- in case of deoxy series i.e.,
dAMP = deoxyadenosine monophosphate
ATP = adenosine triphosphate
UDP = Uridine diphosphate
Ribose Sugar
• The double-bonded oxygen on the first carbon in the linear
form becomes the beta OH that is used to bond to a base unit.
• The OH in the second position serves to distinguish between
the ribose in RNA and the deoxyribose in DNA.
• The OH on the third carbon will bond to the phosphate
group of other nucleotides.
• The OH group on the fourth carbon is involved in the closure
of the ring.
• The OH group on the fifth carbon is what bonds to the
phosphate unit of this particular nucleotide.
The carbon atoms in the ribose portion of a nucleotide are
numbered with primes (1', 2', 3', 4', 5') to distinguish them
from the carbon and nitrogen atoms in the base which are
numbered without primes.
Phosphate Group
DNA is a double helical structure. Its
backbone is made up of a repeated
pattern of a sugar group and a
phosphate group.
The deoxyribose sugars are joined at
both the 3'-hydroxyl and 5'-hydroxyl
groups to phosphate groups in ester
links, also known as
"phosphodiester" bonds.
Watson & Crick Base pairing
Nucleotides
• Nucleotides are phosphoric acid esters of
nucleosides.
Adenosine 5'Monophosphate (AMP)
• Adenosine 5'-monophosphate (AMP) is also
called 5'-adenylic acid.
NH2
N
N
O
5'
HO
P
HO
OCH2 O
N
1'
4'
3'
HO
2'
OH
N
Adenosine Diphosphate
(ADP)
NH2
N
O
HO
P O
HO
N
O
P OCH2 O
N
HO
HO
OH
N
Adenosine Triphosphate
(ATP)
• ATP is an important molecule in several
biochemical processes including:
energy storage (Sections 28.4-28.5)
phosphorylation
NH2
N
O
HO
P
HO
O
O
O
P
HO
N
O
P
OCH2 O
N
HO
HO
OH
N
ATP and Phosphorylation
HOCH2
ATP
+
HO
HO
O
HO
This is the first step in the metabolism
of glucose.
OH
hexokinase
O
ADP +
(HO)2POCH2
HO
HO
O
HO
OH
Joined nucleotides
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PO4
PO4
PO4
PO4
sugar-phosphate + bases
backbone
A molecule of DNA is
formed by millions of
nucleotides joined
together in a long chain
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In fact, the DNA usually consists of a double
strand of nucleotides
The sugar-phosphate chains are on the outside
and the strands are held together by chemical
bonds between the bases
2-stranded DNA
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
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Bonding 1
10
The bases always pair up in the same way
Adenine forms a bond with Thymine
Adenine
Thymine
and Cytosine bonds with Guanine
Cytosine
Guanine
The Double Helix (1953)
8
In fact, the DNA usually consists of a double
strand of nucleotides
The sugar-phosphate chains are on the outside
and the strands are held together by chemical
bonds between the bases
A History of Discovery DNA
• Watson and Crick’s discovery built on the work
of Rosalind Franklin and Erwin Chargaff.
– Franklin’s x-ray images suggested that DNA was a
double helix of even width.
– Chargaff’s rules stated that A=T and C=G.
A History of Discovery DNA
• Chargaff’s Rules
A + G = T + C (Chargaff’s rule)
• Rosalind Franklin’s data provide clues about DNA’s 3-D shape
•
•
•
•
Helix
Width = 2 nm; probably two strands (DOUBLE HELIX)
Nitrogenous bases = 0.34 nM apart
One turn every 3.4 nM (10 base pairs per turn)
• Nobel prize won by Francis Crick, James Watson
&Maurice Wilkins 1962.
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The paired strands are coiled into a spiral called
A DOUBLE HELIX
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THE DOUBLE HELIX
bases
sugar-phosphate
chain
Watson JD and Crick FC
• Watson J.D. and Crick F.H.C. "A Structure for
Deoxyribose Nucleic Acid" Nature 171, 737738 (1953).
• Wilkins M.H.F., Stokes A.R. & Wilson, H.R.
"Molecular Structure of Deoxypentose Nucleic
Acids" Nature 171, 738-740 (1953).
• Franklin R. and Gosling R.G. "Molecular
Configuration in Sodium Thymonucleate"
Nature 171, 740-741 (1953)
Structure of DNA
Sequence of nucleotides is the primary structure.
They bond together in a double-strand which twists
into a double-helix (secondary structure).
This double-helix then wraps around some proteins
(tertiary structure)
Then these coils wrap and fold around each other
and this wrapping and folding continues until the
chromosomes is formed
Polynucleotide chain
Primary Structure of Single Stranded DNA
DNA Polynucleotides
DNA is a normally double stranded directional (antiparallel) macromolecule. Two
polynucleotide chains, held together by weak thermodynamic forces, form a DNA
molecule. Two chains run in opposite directions, Chain has a direction (known as
polarity), 5'- to 3'- from top to bottom.
Features of DNA double helix
(secondary structure)
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





DNA is double stranded: each molecule of DNA is composed of two
polynucleotide chain that are joined together by formation of hydrogen bonds
between the bases.
DNA strands are twisted to form a double helix. The backbone of each consists of
alternating deoxyribose and phosphate groups.
The phosphate group bonded to the 5' carbon atom of one deoxyribose is
covalently bonded to the 3' carbon of the next.
The two strands are "antiparallel"; that is, one strand runs 5′ to 3′ while the other
runs 3′ to 5′
The DNA strands are assembled in the 5′ to 3′ direction
The purine or pyrimidine attached to each deoxyribose projects in toward the axis
of the helix.
Each base forms hydrogen bonds with the one directly opposite it, forming base
pairs .

3.4 Å separate the planes in which adjacent base pairs are located.
 The double helix makes a complete turn in just over 10 nucleotide
pairs, so each turn takes a little more (35.7 Å to be exact) than the
34 Å.
 There is an average of 25 hydrogen bonds within each complete turn
of the double helix providing a stability of binding about as strong
as what a covalent bond would provide.
 The diameter of the helix is 20 Å.
 The path taken by the two backbones forms a major (wider) groove
and a minor (narrower) groove.
Pitch = 3.4 nm
Homologous pairs
Homologous pairs contain identical genes, but
the chromosomes may have different forms of
the genes (alleles).
What is Genome?
Genome of an organism is a sequence of nucleic acid that provides information
needed to construct the organism.
It contains the complete set of hereditary information for any organism.
What is Gene?
Gene is the functional unit of genome. Gene is a sequence of nucleic acid that
produces another nucleic acid.
Gene and Chromosome?
DNA is organized into chromosomes which are found within the nuclei of cells.
Genetic material of living organisms is either DNA or RNA.
DNA – Deoxyribonucleic acid
RNA – Ribonucleic acid
RNA
•Most cellular RNA molecules are single stranded.
many self-complementary regions , RNA commonly exhibits an intricate secondary
structure (relatively short, double helical segments alternated with single stranded
regions)
•complex tertiary interactions fold the RNA in its final three dimensional form.
•Double standed RNA can also exists and is generally similar to A-DNA (present is
few viruses)
RNA structure
Primary structure
A) single stranded regions
formed by unpaired nucleotides
Secondary structure
B) duplex
double helical RNA (A-form with 11 bp per turn)
C
C) hairpin
duplex bridged by a loop of unpaired nucleotides
D) internal loop
D
nucleotides not forming Watson-Crick base pairs
E
G
E) bulge loop
unpaired nucleotides in one strand,
other strand has contiguous base pairing
F
F) junction
B
A
three or more duplexes separated by single
stranded regions
G) pseudoknot
tertiary interaction between bases of hairpin loop
and outside bases
Nucleic acids are DNA and RNA
DNA
• The principal location
of DNA is the nucleus
of eukaryotic cells.
• Secondary locations of
DNA are mitochondria.
RNA
• The different types of
RNA are located in
nucleus, cytoplasm,
mitochondria,
ribosomes.
Three classes of RNA
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
Getting from DNA to protein:
Two parts: 1. Transcription in which a short portion of
chromosomal DNA is used to make a RNA molecule small enough
to leave the nucleus.
2. Translation in which the RNA code is used to
assemble the protein at the ribosome
The “central dogma” of modern biology:
DNA  RNA  protein