Lecture 2 Properties and functions of

nucleic acids

BB10006 – MVH

Reference:Chapter 28 (2e) or 29 (3e)Biochemistry by Voet and Voet

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

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

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

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

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

Supercoiled DNA moves faster than relaxed DNA

Allows packing / unpacking of 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

supercoiled

Relaxed circle

Full length linear

Why does a plasmid that has never been cut give more than one band on a gel?

EBr

Forces stabilising nucleic acid structures

Applications in polymerase chain reaction (PCR)

A) Denaturation and renaturation of DNA

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

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

Forces stabilising nucleic acid structures

Holds together double stranded nucleic acids

Hydrogen bonds do not stabilise DNA

C) Base pairing

Hoogsteen base pairing

Watson-Crick 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

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

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 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)

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 in1) 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