Lecture 2
Properties and functions of nucleic
acids
Reference:
Chapter 28 (2e) or 29 (3e)
Biochemistry by Voet and Voet
BB10006 – MVH
learning objectives
1) Understand the C-value paradox?
2) Be able to describe how the different helical
topologies of DNA contribute to packing?
3) Understand the factors that contribute to the
stability of the DNA double helix?
4) Appreciate the diverse functions of nucleic acids
Lecture 2: Outline
C-value paradox
DNA topology and function
Factors that stabilise DNA
a) denaturation and renaturation
b) Sugar-phosphate chain conformations
c) Base pairing and base stacking
d) hydrophobic and ionic interactions
Functions of nucleic acids
Size of nucleic acids
DNA molecules tend to be larger than RNA
Largest known mammalian gene is
Dystrophin gene (DMD)
2.5 Mbp (0.1% of the genome)
genome sizes
organism
Number of base pairs (kb)
viruses
Lambda bacteriophage ( λ)
bacteria
Eschericia coli
eukaryotes
Yeast
Drosophila
Human
48.6
4,640
13,500
165,000
3.3 x 106
Comparative
genome sizes
Why is there a
discrepancy between
genome size and
genetic complexity?
C-value paradox
Due to the presence of Repetitive DNA
(nonfunctional?)
Repetitive DNA families constitute
nearly one-half of genome (~52%)
Protein domains contribute to
organism complexity
Topology of DNA
DNA supercoiling: coiling of a coil
Important feature in all chromosomes
Allows packing / unpacking of DNA
Supercoiled DNA moves faster than relaxed DNA
negatively supercoiled (right handed)
•
Results from under or unwinding
Important in DNA packing/unpacking e.g during
replication/transcription
•
positively supercoiled (left handed)
•
Results from overwinding
•
Also packs DNA but difficult to unwind
Why does a plasmid that has never been cut give
more than one band on a gel?
Full length linear
Relaxed circle
supercoiled
EBr
Forces stabilising nucleic acid
structures
A) Denaturation and renaturation of DNA
Applications in polymerase chain
reaction (PCR)
Denaturation of DNA
Also called melting
Occurs abruptly at
certain
temperatures
Tm – temp at
which half the
helical structure
is lost
DNA melting curve
Tm varies according to the GC content
High GC
content high Tm
GC rich
regions tend
to be gene
rich
Renaturation of DNA
Also called
annealing
Occurs ~
25oC below
Tm
Property used
in PCR and
hybridisation
techniques
Forces stabilising nucleic acid
structures
B) Sugar-phosphate chain conformations
position on N-glycosidic linkage
Sugar ring pucker
C2’ or C3’ pucker
Endo conformation
(same side as C5’)
B-DNA is C2’ endo
Fig: 28-18
Voet and Voet
Forces stabilising nucleic acid
structures
C) Base pairing
Holds together double stranded
nucleic acids
Hydrogen bonds do not stabilise DNA
Watson-Crick base
pairing
Hoogsteen base pairing
Forces stabilising nucleic acid
structures
D) Base stacking
and
hydrophobic
interactions
Under aqueous conditions,
Bases aggregate due
to the stacking of
planar molecules
This stacking is
stabilised by
hydrophobic forces
Forces stabilising nucleic acid
structures
E) Ionic interactions
Tm of a DNA duplex increases with cationic
concentration
Caused by electrostatic shielding of anionic
phosphate groups
e.g. Mg 2+ more effective than Na+
Functions of nucleic acids
1) Storage of genetic information
2) Storage of chemical energy e.g. ATP
3) Form part of coenzymes
e.g. NAD+, NADP+, FAD and coenzyme A
4) Act as second messengers in signal
transduction e.g. cAMP
Functions of nucleic acids
1) Storage of genetic information
DNA (deoxyribonucleic acid)
DNA is the hereditary molecule in almost
all cellular life forms. It has 2 main
functions
replication (making 2 copies of the
genome) before every cell division
transcription: process of copying a
portion of DNA gene sequence into a
single stranded messenger RNA (mRNA)
RNA (ribonucleic acid)
Has a more varied role. 4 main types of RNA are
1) mRNA: directs the ribosomal synthesis of
polypeptides and other types of RNA
(translation)
2) Ribosomal RNA: have structural & functional
roles
3) Transfer RNA: deliver amino acids during
protein synthesis
4) Ribonucleoproteins: take part in post
transcriptional processing
Functions of nucleic acids
2) Storage of chemical energy e.g. ATP
ATP (adenosine triphosphate)
Involved in
1) Early stages of
nutrient breakdown
2) Physiological
processes
3) Interconversion of
nucleoside
triphosphates
Functions of nucleic acids
3) Form part of coenzymes
e.g. NAD+, NADP+, FAD and coenzyme A
CoA (coenzyme A)
Functions of nucleic acids
4) Act as second messengers in signal
transduction e.g. cAMP
cAMP (cyclic Adenosine
Mono Phosphate)
Primary intracellular signalling molecule
(second messenger system)
Glycogen metabolism
cAMP dependent kinase (cAPK)
Gluconeogenesis
Fatty acid metabolism - thermogenesis