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Chapter 4
Nucleic Acids: the flow of genetic
information
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Nucleic acids: DNA & RNA
DNA to DNA (replication)
DNA to RNA: mRNA, tRNA, & rRNA;
RNA to Protein: Genetic code (Translation);
Introns and exons.
Transcription
DNA
Translation
RNA
Protein
Nucleic acids are linear polymers built up from similar units
connected end to end: a sugar, a phosphate, & a base. Each
base is one of A, T, G, or C and the sequence of bases along
the backbone carries the genetic information.
DNA (deoxyribonucleic
acid) and RNA (ribonucleic
acid) differ in the sugar
component.
The prime next to the
number indicates that it is
part of the sugar and not the
base.
Backbones of DNA and RNA
Phosphodiester linkage
DNA and RNA differ in one of the bases
Nucleotides are the monomeric
units of nucleic acids
A unit consisting of a base bonded to a sugar is called nucleoside.
RNA: adenosine, guanosine, cytidine, & uridine;
DNA: deoxyadenosine, deoxyguanosine, deoxycytidine, & thymidine.
A nucleotide is a nucleoside
joined to one or more phosphate
groups by an ester linkage
ATP: adenosine 5’-triphosphate
Deoxyguanosine 3’-monophosphate
3’-dGMP
The base sequence is written in
the 5’- to 3’ direction
pApCpG or pACG
DNA is a long polymer
In some cases if stretched out it would be a foot long
about 1 billion bp/foot
The DNA double helix structure
James Watson and Francis Crick used Maurice Wilkins and
Rosalind Franklin’s data to propose a DNA structure:
The right handed DNA double helix structure.
Important for the replication of genetic information.
Minor groove
Major groove
Properties of the DNA double
helix
•  Two DNA single strands are coiled around
common axis in the right handed fashion.
The strands run in the opposite directions.
•  The sugar phosphate backbones are on the
outside and, therefore, the purine and
pyrimidine bases lie on the inside of the
helix.
•  The diameter of the helix is 20 Å.
Continue
•  The bases are nearly perpendicular to the helix
axis, and adjacent bases are separated by 3.4 Å.
The helical structure repeats every 34 Å, so there
are 10 base pairs per turn of helix. There is a
rotation of 36 degree per base.
•  The double helix is stabilized by hydrogen bonds
and hydrophobic interactions or base staking.
The Chargaff rule (Erwin Chargaff)
A-T and G-C base pairs have essentially the same shape
Base stacking
Other forms of DNA
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A form DNA.
B form DNA
Z form DNA (left handed DNA).
Water activity.
Z-DNA
Some DNA molecules are
circular and supercoiled
Single stranded nucleic acids
DNA Semiconservative Replication: the
Meselson & Stahl Experiment
Matthew Meselson and Franklin Stahl carried the following experiment:
E. coli grows in a medium containing 15NH4Cl
15N
DNA
Shift to 14NH4Cl medium
Purify DNA
Gradient sedimentation
The double helix can be
reversibly melted
DNA is replicated by DNA
polymerase that take instruction
from templates
(DNA)n + dNTP
(DNA)n+1 + PPi
DNA polymerase requires all 4 dNTPs, a preexisting
template, and a primer with a free 3’ OH.
Elongation proceeds in the 5’ to 3’ direction.
Some polymerases are able to correct mistakes so fidelity is
108
The chain elongation reaction catalyzed by DNA polymerase
Is a nucleophilic attack by the 3’-hydroxyl group of the primer
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Retroviruses use RNA to store genetic information and then
convert the RNA to DNA using reverse transcriptase
Introduction to gene expression
Several kinds of RNA play key
roles in gene expression
•  Messenger RNA (mRNA): template for
protein synthesis (translation),
heterogeneous;
•  Transfer RNA (tRNA): amino acid carriers
for protein synthesis (~ 75 nucleotides);
•  Ribosomal RNA (rRNA): the major
component of ribosomes (the factory to
synthesize proteins).
mRNA is only a small portion of total RNA
Eukaryotic cells contain
additional small RNA molecules
•  Small Nuclear RNA (snRNA), splicing of RNA
exons;
•  Signal recognition particle, protein trafficking
•  Micro RNA (miRNA) ~21 nucleotides, binds to
complementary RNA and inhibits translation
•  Small interfering RNA (siRNA), binds to mRNA
to help degradation
•  Component of telomerase, maintains teleomers
during DNA replication
All cellular RNA is synthesized
by RNA polymerases
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Template: usually double stranded DNA;
NTPs: ATP, GTP, UTP, & CTP;
Mg2+;
RNA polymerase.
(RNA)n + NTP
• NO primer required
(RNA)n+1
RNA polymerases take instruction from
DNA templates, synthesis 5’ to 3’:
Template strand
Coding strand
Transcription begins near promoter sites
ends at terminator sites
Transcription terminator
In eukaryotes mRNA is modified after transcription. A
cap structure is added at the beginning and poly(A) is
added at the end.
Introduction to gene expression
tRNA is the adaptor molecule in protein synthesis:
Aminoacyl-tRNA synthetase
Amino acids are encoded by groups of
three bases starting from a fixed point
•  The genetic code is the relation between the
sequence of bases in DNA or mRNA and
the sequence of amino acids in proteins;
•  Three nucleotides encode an amino acid;
•  The code is nonoverlapping;
•  The code has no punctuation;
•  The code is degenerate: 20 aa vs. 64 codes.
All 64 codons have been deciphered
Major features of the genetic code
•  Only Trp and Met are coded by just one
triplet;
•  Other 18 aa are coded by two or more
codons (synonyms). Most synonyms differ
only on the last base of the triplet (XYU and
XYC always encode the same aa);
•  Degeneracy minimizes the deleterious
effects of mutations.
Proteins are synthesized on
Ribosomes
In bacteria the first amino
acid is fMet, which is
encoded by a specific
tRNA
AUG or GUG is only part of the initial signal
Open reading frame
The genetic code is nearly universal
Most eukaryotic genes are
mosaics of introns and exons
•  Regions that are removed from the primary
transcript are called introns (for intervening
sequences), where as those that are retained
in the mature RNA are called exons (for
expressed regions);
•  Splicing is a reaction to remove introns,
which is carried by spliceosomes;
•  Introns nearly always begins with GU and
end with an AG that is preceded by a
pyrimidine-rich tract. This consensus
sequence is part of the signal for splicing;
•  Many exons encode protein domains.