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Physical Structure and
Replication of DNA
Nature of the Genetic Material
Property 1 - it must contain, in a stable
form, information encoding the organism’s
structure, function, development and
reproduction
 Property 2 - it must replicate accurately so
progeny cells have the same genetic makeup
 Property 3 - it must be capable of some
variation (mutation) to permit evolution
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DNA double helix
1. Sugar-phosphate backbone
2. Base-pair "rungs" of ladder
3. Nucleotides attached to S-P molecules
4. Strands antiparallel (run in opposite directions, 5'-->3')
5. Each base-pair "rung" has a purine (A or G) and pyrimidine
(C or T)
6. Strands held together by hydrogen bonds between
nucleotides
7. Chemical structures of nucleotides discourage "incorrect"
pairing
8. G-C pair has 3 hydrogen bonds, A-T only 2-->former is
stronger
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DNA Structure
How DNA Replicates
DNA Replication
1. Semiconservative = replication results in two DNA
molecules each with two strands, one original and one
new.
2. Sequence of events
a) Helix unwinds
b) Both strands replicate simultaneously, during
unwinding process
c) "Leading" strand replicates continuously from 3' end
of existing strand, with newest end of forming strand
facing into replication fork
d) "Lagging" strand replicates by a series of fragments
placed end-to-end, with newest ends of fragments facing
away from fork; fragments later "ligated"
e) During replication, 2 polymerases "proofread" for
mismatched bases
Replication of DNA and
Chromosomes

Speed of DNA replication:
3,000 nucleotides/min in human
30,000 nucleotides/min in E.coli
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Accuracy of DNA replication:
Very precise (1 error/1,000,000,000 nt)
Process of DNA Replication
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Hydrogen bonds between base pairs are broken
and the two sides of the ladder unzip
Semi-conservative replication: the
original molecule is no longer present
but each new molecule will have
one original strand
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Polymerases (enzymes) link free-floating
nucleotides to their matching base on the
parent strand
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There are estimated to be 3 billion bases in
a human DNA strand
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Mistakes are rare but do happen
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Proofreader enzymes fix most mistakes
DNA has a direction.
It consists of two antiparallel strands with
distinguishable 5′ and 3′ ends
(the numbers refer to the number of the
carbon in the ribose sugar).
→ base
 Carbon-3 → downstream PO4
 Carbon-5 → upstream PO4
 Carbon-1
The original strand of DNA is read in the 3’ to 5’
direction
The new strand is
assembled in the 5’ to 3’ direction
If both sides were synthesized at once, you'd need
two different DNA polymerases:
one for 5′ → 3′;
and one for 3′ → 5′.
However, experimentally, we find that all DNA
polymerases synthesize the new strand 5′ → 3′
The original strand of DNA is read in the 3’ to 5’ direction,
The new strand is assembled in the 5’ to 3’ direction
Since DNA synthesis only occurs in the 5′ and 3′,
so DNA polymerases must move in antiparallel
directions to synthesise the two daughter helices.
Because the synthesis of DNA only occurs in one
direction, different processes must occur on the
two strands.
These two strands are termed the leading and lagging
strands.
The leading strand is synthesised continuously 5′→3′.
However, the other, 'lagging' strand is still
synthesised 5′→3′ but in discrete chunks called
Okazaki fragments, from the replication fork back
towards the origin.
Gene Recombinations
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The process of cutting out damaged or foreign
segments of DNA and repairing them
Restriction enzymes: The scissors that cut
certain segments out of the DNA strand
DNA Ligase: The glue that restores the
damaged segment
New, Improved Mouse
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Scientists have discovered a way to incorporate a
gene that caused cancer into a mouse’s genes.
This allowed the scientists to have a living
model to use to study chemicals which cause
cancer and apply it to humans
DNA fingerprinting
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The use of comparing two samples of DNA to test for
a match
There are particular arrangements along the DNA
molecule that appear to have no function
This DNA segment is taken from a suspect and
compared to the same segment taken from the scene of
the crime.
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If the segments match then the suspect can be arrested.
Only identical twins have the same segments
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Cell Transcription/Translation
DNA Workshop
What is a gene?
Definitions of the gene

The gene is to genetics what the atom is to
chemistry.

The gene is the unit of genetic information that
controls a specific aspect of the phenotype.

The gene is the unit of genetic information that
specifies the synthesis of one polypeptide.
Gene Structure and Function
1. Segments of chromatin that yield proteins through
transcription, translation
2. Typically separated by stretches of inactive
chromatin (intergenic spacers)
3. Commonly encompasses short stretches of inactive
chromatin that get cut out during translation
(introns)
4. Can experience recombination in whole or in part!
(contrary to original theories)
5. Fundamental Components:
a) Promoter Region "upstream" of initiation site:
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Necessary binding site for RNA polymerase to
accomplish translation
Bears recognition sequences for enzyme (e.g., TTTA)
b) Initiation Site for transcription

yields ribosomal binding site in mRNA
c) Coding Region (exon) of structural gene
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Composed of codons (triplets) of nucleotides
Begins with start codon (e.g., TAA)
Ends with stop codon
Codons complementary to mRNA codons 
amino acids in ultimate protein chain
d) Termination Region halts polymerase from
transcribing
1. Transcription from DNA strand in
nucleus
a) Takes place in three areas of DNA strand:
i) One site codes for large and small ribosomal
subunits of rRNA
ii) Second site, downstream, codes for transfer
RNAs (tRNAs)
iii) Third site, further downstream, codes for
proteins
b) Nucleotides assembled parallel to DNA
c) Complementary nucleotides used:
A<-->U, C<-->G
2. Processing of Primary RNA
Transcript from Protein-coding Region
of DNA
a) 5' cap and 3' poly-A tail stuck on
b) introns spliced out in several stages, bringing exons
into proximity
c) Processing in different organs may eliminate
different portions of primary transcript (exons), too
 different mRNA products from same initial
transcript
3. rRNA and tRNAs move into cytoplasm through nuclear
pores immediately
4. Mature mRNA moves into cytoplasm after processing
completed
5. Genes of mature mRNA translated to proteins
a) Ribosomal subunits attach to mRNA (usually several
at different points)
b) tRNAs bring amino acids corresponding to mRNA
codons into proximity of ribosomal complex
c) Amino acids joined by peptide bonds to form protein
chain
6. No "proofreading" functions by RNA polymerases
The Genetic Code
The Genetic Code
A. The code:
 4 nucleotides (organized into triplets  yield 64
possible combinations)
 20 commonly employed amino acids
 Multiple "synonymous" codons for many amino acids
B. Codon-anticodon pairing:
 Third position "wobble"--sloppy pairing for last
nucleotide in codon
 mRNA codons with G or U in third position will
recognize and accept more than one tRNA anticodon
The coding sequence of a gene and its
polypeptide product are colinear
Resources
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From DNA to Protein
DNA and Protein Synthesis in the Cell
Genetics Handbook
Animations at Virtual Cell Biology Classroom
Say it with DNA Protein synthesis tutorial