lecture 2 properties and functions of nucleic acids bb10006 – mvh reference: chapter 28 (2e) or 29...
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Lecture 2 Properties and functions of
nucleic acids
BB10006 – MVH
Reference:Chapter 28 (2e) or 29 (3e)Biochemistry by Voet and Voet
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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
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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
Lecture 2: Outline
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Size of nucleic acids
Largest known mammalian gene is
Dystrophin gene (DMD)
2.5 Mbp (0.1% of the genome)
DNA molecules tend to be larger than RNA
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genome sizes
organism Number of base pairs (kb)
virusesLambda bacteriophage ( λ) 48.6
bacteriaEschericia coli 4,640
eukaryotesYeast 13,500Drosophila 165,000Human 3.3 x 106
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Comparative genome sizes
Why is there a discrepancy between genome size and genetic complexity?
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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
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Topology of DNA
DNA supercoiling: coiling of a coil
Important feature in all chromosomes
Supercoiled DNA moves faster than relaxed DNA
Allows packing / unpacking of DNA
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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
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supercoiled
Relaxed circle
Full length linear
Why does a plasmid that has never been cut give more than one band on a gel?
EBr
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Forces stabilising nucleic acid structures
Applications in polymerase chain reaction (PCR)
A) Denaturation and renaturation of DNA
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Denaturation of DNA
Also called melting
Occurs abruptly at certain temperatures
Tm – temp at which half the helical structure is lost
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DNA melting curve
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Tm varies according to the GC content
High GC content - high Tm
GC rich regions tend to be gene rich
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Renaturation of DNA
Also called annealing
Occurs ~ 25oC below Tm
Property used in PCR and hybridisation techniques
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Forces stabilising nucleic acid structures
B) Sugar-phosphate chain conformations
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Fig: 28-18Voet and Voet
position on N-glycosidic linkage
Sugar ring pucker
C2’ or C3’ puckerEndo conformation (same side as C5’)B-DNA is C2’ endo
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Forces stabilising nucleic acid structures
Holds together double stranded nucleic acids
Hydrogen bonds do not stabilise DNA
C) Base pairing
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Hoogsteen base pairing
Watson-Crick base pairing
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Forces stabilising nucleic acid structures
D) Base stacking and
hydrophobic interactions
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Under aqueous conditions, Bases aggregate
due to the stacking of planar molecules
This stacking is stabilised by hydrophobic forces
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Forces stabilising nucleic acid structures
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+
E) Ionic interactions
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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
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Functions of nucleic acids
1) Storage of genetic information
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DNA (deoxyribonucleic acid)
DNA is the hereditary molecule in almost all cellular life forms. It has 2 main functionsreplication (making 2 copies of the genome) before every cell divisiontranscription: process of copying a portion of DNA gene sequence into a single stranded messenger RNA (mRNA)
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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
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Functions of nucleic acids
2) Storage of chemical energy e.g. ATP
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ATP (adenosine triphosphate)
Involved in1) Early stages of
nutrient breakdown
2) Physiological processes
3) Interconversion of nucleoside triphosphates
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Functions of nucleic acids
3) Form part of coenzymes e.g. NAD+, NADP+, FAD and coenzyme A
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CoA (coenzyme A)
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Functions of nucleic acids
4) Act as second messengers in signal transduction e.g. cAMP
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cAMP (cyclic Adenosine Mono Phosphate)
Primary intracellular signalling molecule
(second messenger system)
Glycogen metabolism
cAMP dependent kinase (cAPK)
Gluconeogenesis
Fatty acid metabolism - thermogenesis
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