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Structure and Function of Nucleic Acids (Seven major types of RNA…
Structure and Function of Nucleic Acids
X-ray diffracion
The rays are bent, or diffracted by the molecules that they encounter and the diffraction pattern is recorded on film
Crystals of a molecule are bombarded with a beam of x-rays
When analysed mathematically the diffraction pattern can yield information about the 3D structure of a molecule
DNA Polynucloetde strands are held together by H bonding between base pairs
Hydrophobic bonding is an example of weak van der waals interactions
There are van der walls interactions between the stacked planer bases inside the DNA
A large number of weak van der waals interactions can significantly increase the stability of a structure, such as the DNA double helix
In a nucleotide the base is hydrophobic inside and there are two hydrophilic groups: A
Negatively charged phosphate and sugar group
The two very hydrophilic groups form H-bonds and will interact strongly with water
The hydrophobic surfaces of the bases are found in the centre of the molecule, whereas the sugars and phosphates at the periphery in contact with water
Stacking arrangement
makes the molecule both compact and very strong
Why negative Charge in DNA
The backbone of polynucleotides are highly charged (1 unit negative charge for each phosphate group; 2 negative charges per base-pair).
The negative charge property is important for interaction with histones (positively charged)
If there was no salt in the medium surrounding DNA, a strong repulsion between the two strands would exist and the strands would fall apart.
Therefore counter-ionsare essential for the double-helical structure. Counter-ions shield the charges on the sugar-phosphate backbone.
The negative charge property of DNA can be utilised for laboratory analysis
DNA can undergo reversible strand separation
Supercoiling of DNA
Supercoils form a twisted 3-D structure which is more favourable energetically
Less stable than relaxed DNA
DNA is restrained when it is supercoiled around DNA - binding proteins
DNA - Virtually prokaryotes and eukaryotes is negatively supercoiled
Some architectural proteins: induce DNA negative supercoiling upon binding.
RNA secondary structure
Because of the extra hydroxyl group on the sugar. RNA is too bulky to form a stable double helix
Hairpin loops can form between complementary base pairs: making it a secondary structure
RNA can contain - noncanonicalbase pairs: widen the major groove and make it more accessible to ligands or proteins
GU Wobble
GA sheared
AU reverse Hoogsteen
GA Imino
Seven major types of RNA
Ribosomal RNA (rRNA)
Functions structural and enzymatic component of ribosomes
Messenger RNA (mRNA)
Acts as intermediate between genetic code of DNA and amino sequence of proteins
Transfer RNA (tRNA)
Adaptor molecule that carries amino acids to specific codon on mRNA in ribosome during protein synthesis
small nuclear RNA (snRNA) in eukaryotes
Involved in removal or splicing of introns from eukaryotic mRNA
MicroRNA (miRNA)
Piwi - interacting RNA (piRNA)
Small RNA, often complementary to untranslated region of mRNA
Short interfering RNA (siRNA)
Recruits RNA-induced silencing complex for mRNA cleavage and gene silencing