Computational Biology I
LSM5191
Aylwin Ng, D.Phil
Lecture 1: Introduction to Nucleic Acids – the
building blocks of life.
DNA & CHROMOSOMES
2m of DNA,
all 3 billion letters in the DNA code,
compacted into 46 chromosomes, and packed into a cell 0.0001cm across!
DNA densely packed into Chromosomes
Flow of Information in Living Systems
Central Dogma of molecular biology:
transcription
DNA

translation
RNA

Protein
DNA Sequence Implies Structure Implies Function
Transcription
mRNA
Transport
Translation
Nascent polypeptide
mRNA
ribosome
Post-transl. modif
functional protein
NUCLEIC ACIDS
 Deoxyribonucleic acid (DNA) contains the information prescribing the
amino acid sequence of proteins.
 This information is arranged in units termed genes.
 A GENE is the entire nucleic acid sequence that is necessary for the
synthesis of a functional polypeptide
 Ribonucleic acid (RNA) serves in the cellular machinery that chooses
and links amino acids in the correct sequence.
 DNA and RNA are polymers of nucleotide subunits
NUCLEOTIDE SUBUNITS
• A nucleotide unit consists of a
pentose sugar, a phosphate
moiety (containing up to 3
phosphate groups) and a
Base.
• Subunits are linked together
by phosphodiester bond, to
form a ‘sugar-phosphate
backbone’:
Nucleotide
Phosphate group
Base
Ribose or
Deoxyribose
(shown here)
NUCLEOTIDES
• All nucleotides have a common structure
BASES
• 5 principal bases in nucleic acids:
A, G, C, T are present in DNA
A, G, C, U are present in RNA
NUCLEOSIDES & NUCLEOTIDES
ELUCIDATING THE STRUCTURE OF DNA
• James Watson (Cambridge University),
• Francis Crick (Cambridge University),
Nobel Prize (Medicine) in 1962
• Maurice Wilkins (King’s College London),
• Rosalind Franklin (King’s College London)
- succeeded in obtaining superior X-ray diffraction data
X-RAY DIFFRACTION
• Data showed that DNA has the form of a regular helix
• Diameter 20 Å (2 nm)
• Making a complete turn every 34 Å (3.4 nm)
 i.e. 10 nucleotides per turn
BASE-PAIRING
Edwin Chargaff’s results (1952):
Base compositions experimentally determined for a variety of organisms
DNA STRUCTURE
• Native DNA (B-form) is a double helix of complementary anti-parallel chains.
• Double helix is right-handed, with turns running clockwise along helical axis.
Hydrogen bonding between complementary base pairs (A-T or G-C) holds the two
strands together
DNA REPLICATION
“It has not escaped our notice that the specific pairing we have
postulated immediately suggests a possible copying mechanism
for the genetic material.”
-Watson & Crick, Nature (1953)
DNA REPLICATION
• DNA replication is semi-conservative.
• IMPLICATION:
the structure of DNA carries information
needed to perpetuate its sequence .
• Demonstrated by Meselson-Stahl (1958)
• Labeled parental DNA with ‘heavy’
density label by growing E. coli in
medium containing isotope (e.g. 15N):
Light (14N)
Hybrid
Heavy (15N)
parental
1st Gen
2nd Gen
NUCLEIC ACID SYNTHESIS
 Both DNA and RNA chains are produced by copying of template DNA
strands.
 Nucleic acid strands grow in the 5’  3’ direction.
 Energetically unfavorable. Driven by energy available in the
triphosphates.
 DNA-dependent RNA polymerases can initiate strand growth but
DNA polymerases require a primer strand.
E. coli DNA polymerases
DNA repair &
replication
Main replicating enzyme
DNA repair
DNA Replication
Clip
http://academy.d20.co.edu/kadets/lundberg/DNA_animations/DNAreplication.mov
BIDIRECTIONAL REPLICATION
• DNA replication proceeds bidirectionally from a given starting site (Origin of
Replication), with both strands being copied at each fork.
Common features of Replication Origins (of E. coli, yeast, SV40)
• Unique segments containing multiple short repeated sequences,
• Short repeated units recognised by multimeric proteins (which assembles DNA
polymerases & replication enzymes),
• Origin regions contain an AT-rich stretch (less energy req.d to melt A.T base pairs).
BIDIRECTIONAL REPLICATION
Key events prior to the replication process (E. coli):
• Binding of DnaA protein at Origin  separate (‘melt’) the strands.
• DnaC & DnaB bind at Origin.
• Then Helicase (DnaB)  unwinding of duplex in opposite directions away from
Origin.
• Unwinding of duplex is an ATP-dependent process.
• Single-strand binding (SSB) protein binds to the single-stranded (ss) DNA,
preventing it from reforming the duplex state.
• Primases (RNA polymerase) bind to DnaB helicase  primosome complex
• Primases dissociate after synthesizing short primer RNAs (complementary to
both strands).
REPLICATION FORK
LAGGING-STRAND SYNTHESIS
TWO or just ONE Polymerase needed?
MAMMALIAN DNA POLYMERASES
Main
replicating
enzyme
Priming
DNA
repair
Mitochond.
DNA
replication
REPLICATION IN EUKARYOTES
• Very similar to replication in bacteria, differing only in details.
• DNA polymerase  has primase activity  generates RNA primers.
• DNA polymerase  is the main replicating enzyme.
• Eukaryotic DNA polymerases appear to lack 5’ 3’ exonuclease activity needed
to remove RNA primer from each Okazaki fragment.
• ‘Flap endonuclease’ (FEN1) initiates primer degradation by associating with
DNA polymerase .
What happens at Telomeres?
Leading strand
Chromosome end
(Telomere)
3’
5’
5’
3’
3’
Parent molecule
5’
Lagging strand
3’
5’
5’
3’
3’
200bp
200bp
200bp
200bp
200bp
5’
3’
5’
3’
2 Daughter
molecules
Missing Okazaki
fragment
5’
5’
3’
Molecule has
become shorter
Next Generation (or
Grand-Daughter)
molecule
The Solution: TELOMERASE
•
•
•
•
Telomeres can be extended by an independent mechanism.
Catalysed by TELOMERASE.
Enzyme consists of both protein & RNA.
RNA is 450 nucleotides long.
• Contains the seq. 5’-CUAACCCUAAC-3’ near its 5’ end.
• Underlined seq. is the reverse complement of the human telomere repeat seq. 5’TTAGGG-3’.
• This allows telomerase to extend the 3’end
a sufficient amount,
• to facilitate priming & synthesis of a new
Okazaki fragment by DNA polymerase 
•  generate a double-stranded end.
How TELOMERASE extends 3’-end