1. Structure and function ofStructure and function of
DNADNA
Dr. Ghada Abou El-EllaDr. Ghada Abou El-Ella
Lecturer of biochemistryLecturer of biochemistry
Faculty of Vet. MedicineFaculty of Vet. Medicine
South Valley UniversitySouth Valley University

2. Central Dogma
DNA ---------→ RNA---------→Protein.DNA ---------→ RNA---------→Protein.
 This unidirectional flow equation represents theThis unidirectional flow equation represents the
Central DogmaCentral Dogma (fundamental law)(fundamental law) of molecularof molecular
biology.biology.
 This is the mechanism whereby inheritedThis is the mechanism whereby inherited
information is used to create actual objects, namelyinformation is used to create actual objects, namely
enzymes and structural proteins.enzymes and structural proteins.
 An exception to the central dogma is that certainAn exception to the central dogma is that certain
viruses (retroviruses) make DNA from RNA using theviruses (retroviruses) make DNA from RNA using the
enzyme reverse transcriptase.enzyme reverse transcriptase.

3. GeneGene Expression
 Genes are DNA sequences that encodeGenes are DNA sequences that encode
proteins (the gene product)proteins (the gene product)
 Gene expression refers to the processGene expression refers to the process
whereby the information contained in geneswhereby the information contained in genes
begins to have effects in the cell.begins to have effects in the cell.
 DNA encodes and transmits the geneticDNA encodes and transmits the genetic
information passed down from parents toinformation passed down from parents to
offspring.offspring.

4. Genetic codeGenetic code
 The alphabet of the genetic code containsThe alphabet of the genetic code contains
only four letters (A,T,G,C).only four letters (A,T,G,C).
 A number of experiments confirmed that theA number of experiments confirmed that the
genetic code is written in 3-letter words, eachgenetic code is written in 3-letter words, each
of which codes for particular amino acid.of which codes for particular amino acid.
 A nucleic acid word (3 nucleotide letters) isA nucleic acid word (3 nucleotide letters) is
referred to as areferred to as a codon.codon.

5. Nucleic acids
Principle information molecule in thePrinciple information molecule in the
cell.cell.
All the genetic codes are carried out onAll the genetic codes are carried out on
the nucleic acids.the nucleic acids.
Nucleic acid is a linear polymer ofNucleic acid is a linear polymer of
nucleotidesnucleotides

6. Nucleotides
Nucleotides are the unit structure ofNucleotides are the unit structure of
nucleic acids.nucleic acids.
Nucleotides composed of 3Nucleotides composed of 3
components:components:
 Nitrogenous base (A, C, G, T or U)Nitrogenous base (A, C, G, T or U)
 Pentose sugarPentose sugar
 PhosphatePhosphate

7. Nitrogenous bases
There are 2 types:There are 2 types:
Purines:Purines:
Two ring structureTwo ring structure
Adenine (A) and Guanine (G)Adenine (A) and Guanine (G)
Pyrimidines:Pyrimidines:
Single ring structureSingle ring structure
Cytosine (C) and Thymine (T) or Uracil (U).Cytosine (C) and Thymine (T) or Uracil (U).

8. Nucleotide bases

9. Types of Nucleic acids
There are 2 types of nucleic acids:There are 2 types of nucleic acids:
1.1. Deoxy-ribonucleic acidDeoxy-ribonucleic acid (DNA)(DNA)
 Pentose Sugar is deoxyribose (no OH at 2’ position)Pentose Sugar is deoxyribose (no OH at 2’ position)
 Bases are Purines (A, G) and Pyrimidine (C, T).Bases are Purines (A, G) and Pyrimidine (C, T).

10. 2.2. Ribonucleic acidRibonucleic acid (RNA)(RNA)
 Pentose Sugar is Ribose.Pentose Sugar is Ribose.
 Bases are Purines (A, G) and Pyrimidines (C, U).Bases are Purines (A, G) and Pyrimidines (C, U).

11. Linear Polymerization of Nucleotides
 Nucleic acids areNucleic acids are
formed of nucleotideformed of nucleotide
polymers.polymers.
 NucleotidesNucleotides
polymerize together bypolymerize together by
phospho-diesterphospho-diester
bondsbonds viavia
condensation reaction.condensation reaction.
 The phospho-diesterThe phospho-diester
bond is formedbond is formed
between:between:
 Hydroxyl (OH) groupHydroxyl (OH) group
of the sugar of oneof the sugar of one
nucleotide.nucleotide.
 Phosphate group ofPhosphate group of
other nucleotideother nucleotide

12. Polymerization of Nucleotides
 The formed polynucleotideThe formed polynucleotide
chain is formed of:chain is formed of:
 Negative (-ve) chargedNegative (-ve) charged
Sugar-Phosphate backbone.Sugar-Phosphate backbone.
 Free 5’ phosphate on oneFree 5’ phosphate on one
end (5’ end)end (5’ end)
 Free 3’ hydroxyl on otherFree 3’ hydroxyl on other
end (3’ end)end (3’ end)
 Nitrogenous bases are notNitrogenous bases are not
in the backbonein the backbone
 Attached to the backboneAttached to the backbone
 Free to pair withFree to pair with
nitrogenous bases of othernitrogenous bases of other
polynucleotide chainpolynucleotide chain

13. Polymerization of Nucleotides
 Nucleic acids are polymers of nucleotides.Nucleic acids are polymers of nucleotides.
 The nucleotides formed of purine orThe nucleotides formed of purine or
pyrimedine bases linked topyrimedine bases linked to phosphorylatedphosphorylated
sugarssugars (nucleotide back bone).(nucleotide back bone).
 The bases are linked to the pentose sugar toThe bases are linked to the pentose sugar to
formform NucleosideNucleoside..
 The nucleotides contain one phosphateThe nucleotides contain one phosphate
group linked to the 5’ carbon of thegroup linked to the 5’ carbon of the
nucleoside.nucleoside.
Nucleotide = Nucleoside + Phosphate groupNucleotide = Nucleoside + Phosphate group

14. N.B.N.B.
 The polymerization of nucleotides to formThe polymerization of nucleotides to form
nucleic acids occur by condensation reactionnucleic acids occur by condensation reaction
by making phospho-diester bond between 5’by making phospho-diester bond between 5’
phosphate group of one nucleotide and 3’phosphate group of one nucleotide and 3’
hydroxyl group of another nucleotide.hydroxyl group of another nucleotide.
 Polynucleotide chains are alwaysPolynucleotide chains are always
synthesized in the 5’ to 3’ direction, with asynthesized in the 5’ to 3’ direction, with a
free nucleotide being added to the 3’ OHfree nucleotide being added to the 3’ OH
group of a growing chain.group of a growing chain.

15. Complementary base pairing
 It is the most important structural feature ofIt is the most important structural feature of
nucleic acidsnucleic acids
 It connects bases of one polynucleotideIt connects bases of one polynucleotide
chain (nucleotide polymer) withchain (nucleotide polymer) with
complementary bases of other chaincomplementary bases of other chain
 Complementary bases are bonded togetherComplementary bases are bonded together
via:via:
 Double hydrogen bond between A and T (DNA), ADouble hydrogen bond between A and T (DNA), A
and U (RNA)and U (RNA) (A═T or A═U)(A═T or A═U)
 Triple H-bond between G and C in both DNA orTriple H-bond between G and C in both DNA or
RNARNA (G≡C)(G≡C)

16. Base pairing

17. Significance of complementarySignificance of complementary
base pairingbase pairing
 The importance of such complementary baseThe importance of such complementary base
pairing is that each strand of DNA can act aspairing is that each strand of DNA can act as
template to direct the synthesis of othertemplate to direct the synthesis of other
strand similar to its complementary one.strand similar to its complementary one.
 ThusThus nucleic acids are uniquely capable ofnucleic acids are uniquely capable of
directing their own self replicationdirecting their own self replication..
 The information carried by DNA and RNAThe information carried by DNA and RNA
direct the synthesis of specific proteinsdirect the synthesis of specific proteins
which control most cellular activities.which control most cellular activities.

18. DNA structureDNA structure
 DNA is a double stranded molecule consists of 2DNA is a double stranded molecule consists of 2
polynucleotide chains running in oppositepolynucleotide chains running in opposite
directions.directions.
 Both strands are complementary to each other.Both strands are complementary to each other.
 The bases are on the inside of the moleculesThe bases are on the inside of the molecules
and the 2 chains are joined together by doubleand the 2 chains are joined together by double
H-bond between A and T and triple H-bondH-bond between A and T and triple H-bond
between C and G.between C and G.
 The base pairing is very specific which make theThe base pairing is very specific which make the
2 strands complementary to each other.2 strands complementary to each other.
 So each strand contain all the requiredSo each strand contain all the required
information for synthesis (replication) of a newinformation for synthesis (replication) of a new
copy to its complementary.copy to its complementary.

19. Forms of DNA
1-1- B-form helixB-form helix::
It is the most common form of DNA inIt is the most common form of DNA in
cells.cells.
Right-handed helixRight-handed helix
Turn every 3.4 nm.Turn every 3.4 nm.
Each turn contain 10 base pairs (the distanceEach turn contain 10 base pairs (the distance
between each 2 successive bases is 0.34 nm)between each 2 successive bases is 0.34 nm)
Contain 2 grooves;Contain 2 grooves;
 Major groove (wide): provide easy access to basesMajor groove (wide): provide easy access to bases
 Minor groove (narrow): provide poor access.Minor groove (narrow): provide poor access.

20. 2-2- A-form DNAA-form DNA::
 Less common form of DNA , more common inLess common form of DNA , more common in
RNARNA
 Right handed helixRight handed helix
 Each turn contain 11 b.p/turnEach turn contain 11 b.p/turn
 Contain 2 different grooves:Contain 2 different grooves:
 Major groove: very deep and narrowMajor groove: very deep and narrow
 Minor groove: very shallow and wide (binding site for RNA)Minor groove: very shallow and wide (binding site for RNA)
3-3- 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.

21. Denaturing and Annealing of DNA
 The DNA double strands can denatured ifThe DNA double strands can denatured if
heated (95ºC) or treated with chemicals.heated (95ºC) or treated with chemicals.
 AT regions denature first (2 H bonds)AT regions denature first (2 H bonds)
 GC regions denature last (3 H bonds)GC regions denature last (3 H bonds)
 DNA denaturation is a reversible process, asDNA denaturation is a reversible process, as
denatured strands can re-annealed again ifdenatured strands can re-annealed again if
cooled.cooled.
 This process can be monitored using theThis process can be monitored using the
hyperchromicity (melting profile).hyperchromicity (melting profile).

22. Hyperchromicity (melting profile)
 It is used to monitor the DNA denaturation andIt is used to monitor the DNA denaturation and
annealing.annealing.
 It is based on the fact that single stranded (SS)It is based on the fact that single stranded (SS)
DNA gives higher absorbtion reading thanDNA gives higher absorbtion reading than
double stranded (DS) at wavelength 260º.double stranded (DS) at wavelength 260º.
 Using melting profile we can differentiateUsing melting profile we can differentiate
between single stranded and double strandedbetween single stranded and double stranded
DNA.DNA.

23. Hyperchromicity (melting profile)
DS
SS
SS
Ab260
Tm
Temperature
Tm (melting temp.): temp. at which 50% of DS DNA denatured to SS
•Heating of SS DNA: little rise of Ab reading
• Heating of DS DNA: high rise of Ab reading
Using melting profile we can differentiate between SS DNA and DS
DNA

24. Melting profile continue…..
Melting profile can be also used to giveMelting profile can be also used to give
an idea about the type of base pair richan idea about the type of base pair rich
areas using the fact that:areas using the fact that:
 A═T rich regions: denatured first (low melting point)A═T rich regions: denatured first (low melting point)
 G≡C rich regions: denatured last (higher meltingG≡C rich regions: denatured last (higher melting
point)point)
DS
SS
GC rich DNA
AT rich DNA
GC/AT DNA
Tm1 Tm2 Tm3
Tm1: Small melting temp. of AT rich
DNA
Tm2: higher melting temp. of AT/GC
equal DNA
Tm3: Highest melting temp. of GC rich
DNA

25. RNA structure
 It is formed of linear polynucleotideIt is formed of linear polynucleotide
 It is generally single strandedIt is generally single stranded
 The pentose sugar is RiboseThe pentose sugar is Ribose
 Uracile (U) replace Thymine (T) in theUracile (U) replace Thymine (T) in the
pyrimidine bases.pyrimidine bases.
Although RNA is generally single stranded,Although RNA is generally single stranded,
intra-molecular H-bond base pairing occurintra-molecular H-bond base pairing occur
between complementary bases on the samebetween complementary bases on the same
molecule (secondary structure)molecule (secondary structure)

26. Types of RNA
 Messenger RNA (mRNA)Messenger RNA (mRNA)::
 Carries genetic information copied from DNA in the form ofCarries genetic information copied from DNA in the form of
a series of 3-base code, each of which specifies a particulara series of 3-base code, each of which specifies a particular
amino acid.amino acid.
 Transfer RNA (tRNA)Transfer RNA (tRNA)::
 It is the key that read the code on the mRNA.It is the key that read the code on the mRNA.
 Each amino acid has its own tRNA, which binds to it andEach amino acid has its own tRNA, which binds to it and
carries it to the growing end of a polypeptide chain.carries it to the growing end of a polypeptide chain.
 Ribosomal RNA (rRNA)Ribosomal RNA (rRNA)::
 Associated with a set of proteins to form the ribosomes.Associated with a set of proteins to form the ribosomes.
 These complex structures, which physically move along theThese complex structures, which physically move along the
mRNA molecule, catalyze the assembly of amino acids intomRNA molecule, catalyze the assembly of amino acids into
protein chain.protein chain.
 They also bind tRNAs that have the specific amino acidsThey also bind tRNAs that have the specific amino acids
according to the code.according to the code.

27. RNA structure
RNA is a single strandedRNA is a single stranded
polynucleotide molecule.polynucleotide molecule.
It can take 3 levels of structure;It can take 3 levels of structure;
Primary: sequence of nucleotidesPrimary: sequence of nucleotides
Secondary: hairpin loops (base pairing)Secondary: hairpin loops (base pairing)
Tertiary: motifs and 3D foldingsTertiary: motifs and 3D foldings

28. RNA structure
Transfer RNA (tRNA) structure

29. DNA ReplicationDNA Replication
 Replication of the DNA molecule is semi-conservative,Replication of the DNA molecule is semi-conservative,
which means that each parent strand serves as awhich means that each parent strand serves as a
template for a new strand and that the two (2) newtemplate for a new strand and that the two (2) new
DNA molecules each have one old and one newDNA molecules each have one old and one new
strand.strand.
 DNA replication requires:DNA replication requires:
 A strand of DNA to serve as aA strand of DNA to serve as a templatetemplate
 SubstratesSubstrates - deoxyribonucleoside triphosphates- deoxyribonucleoside triphosphates
(dATP, dGTP, dCTP, dTTP).(dATP, dGTP, dCTP, dTTP).
 DNA polymeraseDNA polymerase - an enzyme that brings the- an enzyme that brings the
substrates to the DNA strand templatesubstrates to the DNA strand template
 A source ofA source of chemical energychemical energy to drive this synthesisto drive this synthesis
reaction.reaction.

30. DNA ReplicationDNA Replication
 Nucleotides are always added to the growing strandNucleotides are always added to the growing strand
at the 3' end (end with free -OH group).at the 3' end (end with free -OH group).
 The hydroxyl group reacts with the phosphate groupThe hydroxyl group reacts with the phosphate group
on the 5' C of the deoxyribose so the chain growson the 5' C of the deoxyribose so the chain grows
 Energy is released when the bound linking 2 of the 3Energy is released when the bound linking 2 of the 3
phosphate groups to the deoxyribonucleosidephosphate groups to the deoxyribonucleoside
triphosphate breakstriphosphate breaks
 Remaining phosphate group becomes part of theRemaining phosphate group becomes part of the
sugar-phosphate backbonesugar-phosphate backbone

31. Step 1 - Unwinding and ExposingStep 1 - Unwinding and Exposing
StrandsStrands
DNA strands are unwound and opened byDNA strands are unwound and opened by
enzymes calledenzymes called HELICASESHELICASES
Helicases act at specific places calledHelicases act at specific places called
ORIGINS OF REPLICATIONORIGINS OF REPLICATION
Synthesis of new DNA strands proceeds inSynthesis of new DNA strands proceeds in
both directions from an origin of replicationboth directions from an origin of replication
resulting in a bubble withresulting in a bubble with REPLICATIONREPLICATION
FORKSFORKS at each growing point.at each growing point.

32. Step 2 - Priming the StrandStep 2 - Priming the Strand
 In order to begin making a new strand, a helperIn order to begin making a new strand, a helper
strand called astrand called a PRIMERPRIMER is needed to start theis needed to start the
strand.strand.
 DNA polymeraseDNA polymerase, an enzyme, can then add, an enzyme, can then add
nucleotides to the 3' end of the primer.nucleotides to the 3' end of the primer.
 Primer is a short, single strand of RNA (ribonucleicPrimer is a short, single strand of RNA (ribonucleic
acid) and is complimentary to the DNA templateacid) and is complimentary to the DNA template
strand.strand.
 Primers are formed by enzymes calledPrimers are formed by enzymes called PRIMASES.PRIMASES.

33. Step 3 - Strand ElongationStep 3 - Strand Elongation
 DNA Polymerase IIIDNA Polymerase III catalyses elongation of newcatalyses elongation of new
DNA strands in prokaryotesDNA strands in prokaryotes
 Two molecules of DNA polymerase III clampTwo molecules of DNA polymerase III clamp
together at the replication forks, each acting on 1together at the replication forks, each acting on 1
of the strandsof the strands
 One strand exposed at its 3' end produces aOne strand exposed at its 3' end produces a
daughter strand which elongates from its 5' to 3'daughter strand which elongates from its 5' to 3'
end and is called the LEADING STRAND. Thisend and is called the LEADING STRAND. This
strand is synthesized continuously and growsstrand is synthesized continuously and grows
from 5' to 3'.from 5' to 3'.

34. Step 3 - Strand ElongationStep 3 - Strand Elongation
 The second daughter strand is called theThe second daughter strand is called the
LAGGING STRANDLAGGING STRAND and is antiparallel to theand is antiparallel to the
leading strand. It’s template is exposed from theleading strand. It’s template is exposed from the
5' to 3' end but it must direct the 5' to 3' synthesis5' to 3' end but it must direct the 5' to 3' synthesis
of the lagging strands, since nucleotides areof the lagging strands, since nucleotides are
added at the 3' end of the chain.added at the 3' end of the chain.
 The lagging strand is constructed in small,The lagging strand is constructed in small,
backward directed bits consisting ofbackward directed bits consisting of
discontinuous sections of 100-200 nucleotides indiscontinuous sections of 100-200 nucleotides in
eukaryotes and 1000-2000 nucleotides ineukaryotes and 1000-2000 nucleotides in
prokaryotes, calledprokaryotes, called OKAZAKI FRAGMENTSOKAZAKI FRAGMENTS..

35. Step 3 - Strand ElongationStep 3 - Strand Elongation
 When anWhen an Okazaki fragmentOkazaki fragment forms:forms:
DNA polymerase IDNA polymerase I removes the RNA primer andremoves the RNA primer and
replaces it with DNA adjacent to the fragment.replaces it with DNA adjacent to the fragment.
 leaving 1 bond between adjacent fragmentsleaving 1 bond between adjacent fragments
missing.missing.
 A second enzyme called aA second enzyme called a DNA LIGASEDNA LIGASE
catalyses the formation of the final bond.catalyses the formation of the final bond.

36. 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.