Structure and Function of DNA

Structure and
Function of DNA
Central Dogma
DNA ---------→ RNA---------→Protein.
 This unidirectional flow equation represents the
Central Dogma (fundamental law) of molecular
biology.
 This is the mechanism whereby inherited
information is used to create actual objects, namely
enzymes and structural proteins.
 An exception to the central dogma is that certain

viruses (retroviruses) make DNA from RNA using the
enzyme reverse transcriptase.
Gene Expression
 Genes are DNA sequences that encode
proteins (the gene product)
 Gene expression refers to the process

whereby the information contained in genes
begins to have effects in the cell.
 DNA encodes and transmits the genetic

information passed down from parents to
offspring.
Genetic code
 The alphabet of the genetic code contains
only four letters (A,T,G,C).
 A number of experiments confirmed that the

genetic code is written in 3-letter words, each
of which codes for particular amino acid.
 A nucleic acid word (3 nucleotide letters) is

referred to as a codon.
Nucleic acids
 Principle information molecule in the
cell.
 All the genetic codes are carried out on

the nucleic acids.
 Nucleic acid is a linear polymer of

nucleotides
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:
 Singlering structure
 Cytosine (C) and Thymine (T) or Uracil (U).
Nucleotide bases
Types of Nucleic acids
There are 2 types of nucleic acids:
1. Deoxy-ribonucleic acid (DNA)
 Pentose Sugar is deoxyribose (no OH at 2’ position)
 Bases are Purines (A, G) and Pyrimidine (C, T).
2. Ribonucleic acid (RNA)
 Pentose Sugar is Ribose.
 Bases are Purines (A, G) and Pyrimidines (C, U).
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 information carried by DNA and RNA

direct the synthesis of specific proteins
which control most cellular activities.
DNA structure
 DNA is a double stranded molecule consists of 2
polynucleotide chains running in opposite
directions.
 Both strands are complementary to each other.
 The bases are on the inside of the molecules
and the 2 chains are joined together by double
H-bond between A and T and triple H-bond
between C and G.
 The base pairing is very specific which make the
2 strands complementary to each other.
 So each strand contain all the required
information for synthesis (replication) of a new
copy to its complementary.
Forms of DNA
1- B-form helix:
 Itis 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)
 Contain 2 grooves;
 Major groove (wide): provide easy access to bases
 Minor groove (narrow): provide poor access.
2- A-form DNA:
 Less common form of DNA , more common in
RNA
 Right handed helix
 Each turn contain 11 b.p/turn
 Contain 2 different grooves:
 Major groove: very deep and narrow
 Minor groove: very shallow and wide (binding site for RNA)
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.
Denaturing and Annealing of DNA
 The DNA double strands can denatured if
heated (95ºC) or treated with chemicals.
 AT regions denature first (2 H bonds)
 GC regions denature last (3 H bonds)
 DNA denaturation is a reversible process, as

denatured strands can re-annealed again if
cooled.
 This process can be monitored using the

hyperchromicity (melting profile).
RNA structure
 It is formed of linear polynucleotide
 It is generally single stranded
 The pentose sugar is Ribose
 Uracile (U) replace Thymine (T) in the
pyrimidine bases.
Although RNA is generally single stranded,

intra-molecular H-bond base pairing occur
between complementary bases on the same
molecule (secondary structure)
Types of RNA
 Messenger RNA (mRNA):
 Carries genetic information copied from DNA in the form of
a series of 3-base code, each of which specifies a particular
amino acid.
 Transfer RNA (tRNA):
 It is the key that read the code on the mRNA.
 Each amino acid has its own tRNA, which binds to it and
carries it to the growing end of a polypeptide chain.
 Ribosomal RNA (rRNA):
 Associated with a set of proteins to form the ribosomes.
 These complex structures, which physically move along the
mRNA molecule, catalyze the assembly of amino acids into
protein chain.
 They also bind tRNAs that have the specific amino acids
according to the code.
RNA structure
 RNA is a single stranded
polynucleotide molecule.
 It can take 3 levels of structure;

 Primary: sequence of nucleotides
 Secondary: hairpin loops (base pairing)
 Tertiary: motifs and 3D foldings
RNA structure
Transfer RNA (tRNA) structure

DNA Replication
 Replication of the DNA molecule is semi-conservative,
which means that each parent strand serves as a
template for a new strand and that the two (2) new
DNA molecules each have one old and one new
strand.
 DNA replication requires:

 A strand of DNA to serve as a template
 Substrates - deoxyribonucleoside triphosphates
(dATP, dGTP, dCTP, dTTP).
 DNA polymerase - an enzyme that brings the
substrates to the DNA strand template
 A source of chemical energy to drive this synthesis
reaction.
DNA Replication
 Nucleotides are always added to the growing strand
 The hydroxyl group reacts with the phosphate group
on the 5' C of the deoxyribose so the chain grows
 Energy is released when the bound linking 2 of the 3

phosphate groups to the deoxyribonucleoside
triphosphate breaks
 Remaining phosphate group becomes part of the

sugar-phosphate backbone
Step 1 - Unwinding and Exposing
Strands
 DNAstrands are unwound and opened by
enzymes called HELICASES
 Helicases
act at specific places called
ORIGINS OF REPLICATION
 Synthesis of new DNA strands proceeds in

both directions from an origin of replication
resulting in a bubble with REPLICATION
FORKS at each growing point.
Step 2 - Priming the Strand
 In order to begin making a new strand, a helper
strand called a PRIMER is needed to start the
strand.
 DNA polymerase, an enzyme, can then add

nucleotides to the 3' end of the primer.
 Primer is a short, single strand of RNA (ribonucleic

acid) and is complimentary to the DNA template
strand.
 Primers are formed by enzymes called PRIMASES.

Step 3 - Strand Elongation
 DNA Polymerase III catalyses elongation of new
DNA strands in prokaryotes
 Two molecules of DNA polymerase III clamp

together at the replication forks, each acting on 1
of the strands
 One strand exposed at its 3' end produces a

daughter strand which elongates from its 5' to 3'
end and is called the LEADING STRAND. This
strand is synthesized continuously and grows
from 5' to 3'.
 The second daughter strand is called the
LAGGING STRAND and is antiparallel to the
leading strand.
 The lagging strand is constructed in small,

backward directed bits called OKAZAKI
FRAGMENTS.
When an Okazaki fragment forms:
DNA polymerase I removes the RNA primer and
replaces it with DNA adjacent to the fragment.
 leaving 1 bond between adjacent fragments

missing.
 A second enzyme called a DNA LIGASE

catalyses the formation of the final bond.
Telomerase
 Telomerase is a reverse transcriptase that contain
an RNA template, adds nucleotides to the 3’end of
the lagging-strand template and thus prevents
shortening of lagging strands during replication of
linear DNA molecules such as those of eukaryotic
chromosomes.

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Structure and Function of DNA

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Structure and

 An exception to the central dogma is that certain

 Gene expression refers to the process

 DNA encodes and transmits the genetic

 A number of experiments confirmed that the

 A nucleic acid word (3 nucleotide letters) is

 All the genetic codes are carried out on

 Nucleic acid is a linear polymer of

 Thus nucleic acids are uniquely capable of

 The information carried by DNA and RNA

 DNA denaturation is a reversible process, as

 This process can be monitored using the

Although RNA is generally single stranded,

 It can take 3 levels of structure;

Transfer RNA (tRNA) structure

 DNA replication requires:

 Energy is released when the bound linking 2 of the 3

 Remaining phosphate group becomes part of the

 Synthesis of new DNA strands proceeds in

 DNA polymerase, an enzyme, can then add

 Primer is a short, single strand of RNA (ribonucleic

 Primers are formed by enzymes called PRIMASES.

 Two molecules of DNA polymerase III clamp

 One strand exposed at its 3' end produces a

 The lagging strand is constructed in small,

 leaving 1 bond between adjacent fragments

 A second enzyme called a DNA LIGASE

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