Question

12. What is the 5’ cap, and what does it do? What happens if the 3’ polyA tail is removed from an mRNA molecule? Why would an endonuclease cleavage site in the 3’UTR of an mRNA be highly conserved? Where does translation initiate? What causes termination of translation?

13. Rate the following in terms of stability (energy level): a partially folded protein, a properly folded protein (native state), a partially misfolded protein, amyloid fibrils.

Answer 1

12.
The 5’ cap is a specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA . It is the 5-methyl guanosine cap. The 5’ cap protects the nascent mRNA from degradation and assists in ribosome binding during translation.
If poly A tail is removed from the end of mRNA, decapping complex removes the 5' cap, leading to a degradation of the RNA.
The untranslated regions (UTRs) at the 3'end of mRNA transcripts contain important sequences. 3′ untranslated region (3′UTR) is the region, which is present between the stop codon and the start of the poly(A) tail. UTRs are conserved through species. They influence the fate of mRNA, which in turn influence the protein synthesis.
The interplay of UTRs is crucial for the post-transcriptional regulation of gene expression. So they are conserved.
Translation ends I a process called termination. Termination occurs when a stop codon in the mRNA (UAA, UAG, or UGA) enters the A site of the translational machinery.
For translation to start the start codon 5’AUG must be recognised. Initiation of translation occurs when mRNA, tRNA, and an amino acid meet up inside the ribosome.

13.
Protein folding is the physical process by which a protein chain acquires its native 3-dimensional structure, a conformation that is usually biologically functional, in an expeditious and reproducible manner
Each protein exists as an unfolded polypeptide or random coil when translated from a sequence of mRNA to a linear chain of amino acids. This polypeptide lacks stability.
Failure to fold properly into native structure generally produces inactive proteins, because of lack of stability.
misfolded proteins have modified or toxic functionality.
Amyloid fibrils are formed by normally soluble proteins, which assemble to form insoluble fibers that are resistant to degradation.The amyloid fibrils are deposited extracellularly in the tissues and are thought to have a pathogenic effect.