1. Lecture 2 Properties and functions of nucleic acids
Reference:
Chapter 28 (2e) or 29 (3e)
Biochemistry by Voet and Voet
BB10006 – MVH

2. 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

3. 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

4. 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)

5. genome sizes organism Number of base pairs (kb) viruses
organism Number of base pairs (kb)
viruses
Lambda bacteriophage ( λ) 48.6
bacteria
Eschericia coli 4,640
eukaryotes
Yeast ,500
Drosophila ,000
Human x 106

6. Comparative genome sizes
Why is there a discrepancy between
genome size and
genetic complexity?

7. Protein domains contribute to organism 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

8. 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

9. 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

11. Why does a plasmid that has never been cut give
more than one band on a gel?
Full length linear
Relaxed circle
supercoiled
EBr

12. Forces stabilising nucleic acid structures
Applications in polymerase chain reaction (PCR)
A) Denaturation and renaturation of DNA

13. Denaturation of DNA Also called melting
Occurs abruptly at certain temperatures
Tm – temp at which half the helical structure is lost

14. DNA melting curve

15. Tm varies according to the GC content
High GC content - high Tm
GC rich regions tend to be gene rich

16. Renaturation of DNA Also called annealing Occurs ~ 25oC below Tm
Property used in PCR and hybridisation techniques

18. Forces stabilising nucleic acid structures
B) Sugar-phosphate chain conformations

19. 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

20. Forces stabilising nucleic acid structures
Holds together double stranded nucleic acids
Hydrogen bonds do not stabilise DNA
C) Base pairing

21. Watson-Crick base pairing
Hoogsteen base pairing

22. Forces stabilising nucleic acid structures
D) Base stacking and hydrophobic interactions

23. Under aqueous conditions,
Bases aggregate due to the stacking of planar molecules
This stacking is stabilised by hydrophobic forces

24. 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

25. 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

26. Functions of nucleic acids
1) Storage of genetic information

27. 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)

28. RNA (ribonucleic acid)
Has a more varied role. 4 main types of RNA are
mRNA: directs the ribosomal synthesis of polypeptides and other types of RNA (translation)
Ribosomal RNA: have structural & functional roles
Transfer RNA: deliver amino acids during protein synthesis
Ribonucleoproteins: take part in post transcriptional processing

29. Functions of nucleic acids
2) Storage of chemical energy e.g. ATP

30. ATP (adenosine triphosphate)
Involved in
1) Early stages of nutrient breakdown
2) Physiological processes
3) Interconversion of nucleoside triphosphates

31. Functions of nucleic acids
3) Form part of coenzymes
e.g. NAD+, NADP+, FAD and coenzyme A

32. CoA (coenzyme A)

33. Functions of nucleic acids
4) Act as second messengers in signal transduction e.g. cAMP

34. cAMP (cyclic Adenosine Mono Phosphate)
Primary intracellular signalling molecule (second messenger system)
Glycogen metabolism
cAMP dependent kinase (cAPK)
Gluconeogenesis
Fatty acid metabolism - thermogenesis