TOPIC 6 DNA Backbone

● Phosphate + Deoxyribose
NUCLEIC ACIDS
● Unbranched polymer RNA Backbone
● Has monomer units called ● Phosphate
nucleotides ● Ribose
● Ex:
○ Deoxyribonucleic acid Hydrogen bond
(DNA) ● stabilizes the double helix
○ Ribonucleic acid (RNA) together

Friedrich Miescher FORMS OF DNA DOUBLE HELIX

● Discovered nucleic acids in ● A - DNA
1869 ● B - DNA
● Z - DNA
James Dewey Watson
Francis Crick A - DNA
● Coined DNA molecule as a 3D ● Right Handed
double helix structure ● Major Groove
○ Narrow & Deep
Nucleotide ● Minor Groove
● Building Block ○ Wide & Shallow
1. Pentose Sugar ● 11 base pairs
2. Nitrogenous Bases ● Found in DNA-RNA or RNA-RNA
3. Phosphate
B - DNA
Nucleoside ● Right Handed
● Sugar + Base ● Major Groove
○ Wide & Deep
Nucleotide
● Minor Groove
● Nucleoside + Phosphate
○ Narrow & Deep
● 10 base pairs
Pyrimidine
● Found in Chromosomal DNA
● Cytosine (C)
● Thymine (T)
Z - DNA
● Uracil (U)
● Left Handed
● Major Groove
Purine
○ Flat
● Adenosine (A)
● Minor Groove
● Guanine (G)
○ Narrow & Deep
● 12 base pairs
Nucleic Acid Backbone
● Phosphate + Sugar ● Found in Purines & Pyrimidines
Purine and Pyrimidine bases
● hydrophobic in nature
Prokaryotic DNA
● Found in Cytoplasm
● 1 copy of genome
● Small number of genes
● Single chromosomes
● Not packed with histones
● Circular chromosomes
● Introns are absent
● Replication occurs in
cytoplasm
● Single origin
● Replication is rapid
Eukaryotic DNA
● Found in nucleus
● More than 1 copy of genome
● Large number of genes
● Many chromosomes
● Packed with histones
● Linear chromosomes
● Introns are present
● Replication occurs in the
Nucleus
● Many origin
● Replication is Slow
Negative supercoil
● strands are underwound
● favors unwinding
Positive supercoil
● strands are overwound
● Favors overwinding
Topoisomerase
● changing the supercoiled state
of DNA
Class 1 topoisomerase
● cut the phosphodiester
backbone of one strand of
DNA
Class II topoisomerase
● cut both strands of DNA
DNA gyrase
● bacterial topoisomerase that
introduces negative supercoils
into DNA
● Rejoins the DNA ends
SUPERCOILING IN EUKARYOTIC DNA
● More complicated
Chromatin
● complex of DNA and protein
Histones
● principal proteins in chromatin
● large number of basic AA
residue
In chromatin structure, the DNA is
tightly bound to all types of histone
except H1
Nucleosome
● globular structure in
chromatin
Chromosomes
● individual DNA molecule
bound to a group of proteins
● 15% by mass DNA
● 85% by mass proteins
DENATURATION OF DNA
● carried out by heating the DNA
● also called melting
● bases absorb light in the 260
nm wavelength
● Hyperchromicity
○ increase of absorbance
● Annealing
○ Renaturation of
denatured DNA
DNA Replication
● DNA molecules produce exact
duplicates of themselves
REPLICATION OF DNA
Prokaryotic
● Occurs in cytoplasm
● Single origin
● 2 opposing ends
● 1 or 2 types of polymerase
● DNA Polymerase 3 carries out:
○ Initiation
○ Elongation
● DNA Polymerase 1
○ DNA repair
○ Gap Filling
● Okazaki fragments are large
● Rapid
● DNA gyrase is needed
● Occurs almost continuously
Eukaryotic
● Occurs inside the nucleus
● Numerous origin
● Unidirectional replication
● 4 or more polymerase
● DNA Polymerase α
○ Initiation
● DNA Polymerase δ & ε
○ Elongation
● DNA Polymerase β
○ DNA repair
○ Gap Filling
● Okazaki fragments are short
● Slow
● DNA gyrase is not needed
● Only undergo DNA replication
during the S-phase
DNA
● genetic master plan
RNA
● the “working copies” of the DNA
● it does not contain equal
amounts of specific bases
TYPES OF RNA Genetic code
● assignment of the 64 mRNA
Heterogenous nuclear RNA (hnRNA) codons
● formed directly by DNA
transcription Codon
● three-nucleotide sequence in
Small nuclear RNA (snRNA) an mRNA molecules
● conversion of heterogeneous
nuclear RNA to messenger tRNA
RNA. ● a cloverleaf shape
● function as intermediaries that
Messenger RNA (mRNA) delivers amino acids to the
● carries instructions mRNA

Ribosomal RNA (rRNA) TRANSLATION: PROTEIN SYNTHESIS

● combines with specific proteins
to form ribosomes Substances needed:
● Most abundant type of RNA 1. mRNA molecules
2. tRNA molecules
Transfer RNA (tRNA) 3. amino acids
● delivers amino acids 4. Ribosomes
5. number of different enzymes
Transcription
● DNA directs the synthesis of Five general steps:
hnRNA/mRNA molecules 1. Activation of tRNA
2. Initiation
Gene 3. Elongation
● contains the base sequence 4. Termination
for the production of a specific 5. Post-translational processing
hnRNA/mRNA molecules
● in humans, composed of P site
1000 – 3500 nucleotide units ● peptidyl site

Genome A site
● all of the genetic material ● Aminoacyl site
contained in the chromosomes
of an organism Translocation
● ribosome moves down an
Exon mRNA molecule
● Conveys genetic information

Intron
● does not conveys genetic
information
ANTIBIOTICS Frameshift mutation
● a mutation that inserts or
Erythromycin deletes a base in a molecule
● Binds to the larger bacterial base sequence.
ribosome subunit ● the resulting protein is usually
nonfunctional
Terramycin
● Blocks the A-site location Deletions
● Chromosome segment lost
Streptomycin
● Binds to the smaller bacterial Translocation
ribosome unit ● Segment from chromosome is
transferred to another
Neomycin
● Similar to streptomycin Duplication
● Duplicate of some genes
Chloramphenicol
● Binds to the ribosome Inversion
● Chromosome are is inverted
Mutation
● an error in base sequence

DNA Mutation
● Permanent alteration of DNA
sequence

Chromosome Mutation
● Alterations that affect whole
chromosomes

Mutagen
● substance or agent that
causes a change in the
structure of gene

POINT MUTATION
● one base in a DNA sequence is
replaced with another base

Substitution
● one base is incorrectly added
during replication
DNA REPLICATION
● is semiconservative
● 2 DNA strands are anti parallel
● DNA has complementary base
pairing
● Hydrogen Bonds hold
nucleotides together

DNA Replication
● Proceeds bidirectionally
● Helicase separates the DNA
strands
● Topoisomerase (DNA gyrase)
reduces torsional strain
● SSB (single stranded binding)
proteins stabilizes the isolated
strands
● Requires a RNA primer to begin
● DNA Polymerase 3 adds
nucleotides in the 5’ to 3’
direction
● Semi Discontinuous
● DNA polymerase 1 removes the
RNA primer and replaces it
with DNA
● DNA ligase seals the nick
(okazaki fragments) after the
primer is replaced
● DNA Polymerase 1 & 3 have 3’ to
5’ exonuclease activity
(proofreading)
● DNA polymerase 1 has 5’ to 3’
exonuclease activity (DNA
repair)