Secondary structure of tRNA:
This refers to the arrangement of the chain of the molecule to enable it to function in a proper way. Many models have been proposed for the secondary structure of tRNA. Of these, clover leaf model proposed by Holley (1966) is most widely accepted.
According to the clover leaf model, the single chain of tRNA is folded on itself to form five arms. As a result of this folding, the 3′ end and 5′ end lie adjacent to each other. Each arm consists of a basal stalk, and a loop. The double stranded stalks show the typical base pairing.
There could be an exceptional mismatch.. The loops do not have base pairing. One of the arms which do not have a loop is called the acceptor as this is the binding site for amino acids.
The second arm is called the DNA arm. This has a synthetase site which recognises the amino acid activating enzyme. The fourth is a variable arm; it has a stem, but the loop may or may not be present. The T arm has a ribosome recognition site.
There is also a tertiary structure to the rRNA. This is brought about by H bonding between bases, and between bases and sugar phosphate backbone.
Explain the method of replication in DNA in eukaryotes? DNA replication usually takes place during interphase between two mitotic cycles. According to Watson and Crick whose model has a beautiful inbuilt mechanism of replication, the two coils of the molecule get separated due to the disruption of hydrogen bonds between base pairs.
The two strands separate and unwind. The replication usually starts at a specific point called origin. According to some, the replication begins with an incision made by an enzyme. The unwinding of the coils separates the base pairs. The nucleus consists of many free nucleotides.
These are attracted to the complementary nucleotides on the strands and polymerization begins. The original helix acts as a template. The nucleotides freshly added to the template form their own helical back bone with the help of sugar and phosphate.
The initiation of DNA synthesis requires an RNA primer. This is synthesised by the DNA close to the replication site. This is catalysed by RNA polymerase. The nucleotides are added to the template with the help of DNA polymerase. The RNA primer is degraded while another DNA polymerase enzyme releases the DNA strand.
The synthesis originally of RNA primer is necessary since DNA cannot initiate by itself the formation of a new chain. Replication is discontinuous and produces short fragments of DNA called Okazakifragments in some instances a continuous replication may also take place. The Okazaki fragments later join to form long strands with the help of the enzyme polynucleotide ligase. Replication may be in one direction or in both directions.
Models of republication in eukaryotes:
The linear DNA molecule in eukaryotic organisms can theoretically replicate according to any one of the following types suggested by Delbruck. These are Conservative, Semi conservative and Dispersive.
According to the conservative model, of the two molecules of double helices of DNA formed after replication, one would be completely new and the other completely old. The parent helix remains unchanged.
In the semi conservative model supported by Crick and Watson, each strand of the two molecules of DNA formed after replication would have one old strand and one new strand. This is quite possible because the original DNA strand acts as a template and the newly formed chain binds to the old strand. The dispersive model of replication suggests that the DNA helix breaks at several points forming many fragments. Each fragment would replicate and the fragments rejoin randomly to form two double helices. Each double helix has a mosaic of old and new fragments of DNA.