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   organism Number of base pairs (kb) viruses Lambda bacteriophage ( λ) 48.6 bacteria Eschericia coli 4,640 eukaryotes Yeast 13,500 Drosophila 165,000 Human 3.3 x 106  

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

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

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 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

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 Holds together double stranded nucleic acids Hydrogen bonds do not stabilise DNA C) Base pairing

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 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 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 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

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