Q. No. 1. How can RNA be distinguished from DNA?

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1 Frequently asked questions (FAQS): Q. No. 1. How can RNA be distinguished from DNA? Ans. RNA and DNA are both nucleic acids, but differ in three main ways. First, unlike DNA which is generally double-stranded, RNA is a single-stranded molecule in many of its biological roles and has a much shorter chain of nucleotides. Second, while DNA contains deoxyribose, RNA contains ribose (there is no hydroxyl group attached to the pentose ring in the 2' position in DNA). These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis. Third, the complementary base to adenine is not thymine, as it is in DNA, but rather uracil, which is an unmethylated form of thymine. Q.No.2. Describe the chemical structure of RNA. Ans. Unlike DNA, RNA is single stranded made up of nucleotides arranged in the form of a chain. Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, generally adenine (A), cytosine (C), guanine (G) or uracil (U). Adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3' position of one ribose and the 5' position of the next. The phosphate groups have a negative charge each at physiological ph, making RNA a charged molecule (polyanion). The bases may form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil. However other interactions are also possible, such as a group of adenine bases binding to each other to form bulge.

2 Fig. Chemical structure of RNA Q.No. 3. Describe briefly the synthesis of RNA? Ana. Synthesis of RNA is usually catalyzed by an enzyme RNA polymerase, using DNA as a template, a process known as transcription. Transcription begins with the binding of the enzyme to a promoter sequence in the DNA (usually found "upstream" of a gene). The DNA double helix is unwound by the helicase activity of the enzyme. The enzyme then progresses along the template strand in the 3 to 5 direction, synthesizing a complementary RNA molecule, with elongation occurring in the 5 to 3 direction. The DNA sequence also dictates where termination of RNA synthesis will occur. Q.No. 4. Explain the life-cycle of mrna? Ans. The brief existence of an mrna molecule begins with transcription and ultimately ends in degradation.

3 During its life, an mrna molecule may also be processed, edited, and transported prior to translation. Eukaryotic mrna molecules often require extensive processing and transport, while prokaryotic molecules do not. During transcription, RNA polymerase makes a copy of a gene from the DNA to mrna as needed. This process is similar in eukaryotes and prokaryotes. One notable difference, however, is that prokaryotic RNA polymerase associates with mrna processing enzymes during transcription so that processing can proceed quickly after the start of transcription. The short-lived, unprocessed or partially processed, product is termed pre-mrna; once completely processed, it is termed mature mrna. A fully processed mrna includes a 5' cap, 5' UTR, coding region, 3' UTR, and poly(a) tail. The mature mrna is finally degraded with certain enzymes like nucleases. Q. No. 5. Explain briefly the function of mrna? Ans. It is a molecule of RNA encoding a chemical "blueprint" for a protein product. mrna is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein. In mrna as in DNA, genetic information is encoded in the sequence of nucleotides arranged into codons consisting of three bases each. Each codon encodes for a specific amino acid, except the stop codons that terminate protein synthesis. This process requires two other types of RNA: transfer RNA (trna) mediates recognition of the codon and provides the corresponding amino acid, while

4 ribosomal RNA (rrna) is the central component of the ribosome's protein manufacturing machinery. Q. No.6. Draw the labelled structure of eukaryotic mature mrna? Fig. Structure of a mature eukaryotic mrna. Q.No.7. What are UTRs and what is their function? Ans. Untranslated regions (UTRs) are sections of the mrna before the start codon and after the stop codon that are not translated, termed the five prime untranslated region (5' UTR) and three prime untranslated region (3' UTR), respectively. These regions are transcribed with the coding region and thus are exonic as they are present in the mature mrna. Several roles in gene expression have been attributed to the untranslated regions, including mrna stability, mrna localization, and translational efficiency. The ability of a UTR to perform these functions depends on the sequence of the UTR and can differ between mrnas. The stability of mrnas may be controlled by the 5' UTR and/or 3' UTR due to varying affinity for RNA degrading enzymes called ribonucleases and for the proteins that can promote or

5 inhibit RNA degradation. Translational efficiency, including sometimes the complete inhibition of translation, can be controlled by UTRs. Proteins that bind to either the 3' or 5' UTR may affect translation by influencing the ribosome's ability to bind to the mrna. Cytoplasmic localization of mrna is thought to be a function of the 3' UTR. Proteins that are needed in a particular region of the cell can actually be translated there; in such a case, the 3' UTR may contain sequences that allow the transcript to be localized to this region for translation. Q. No. 8. What are non-sense codons? Ans. Non-sense codons are also called termination codons or stop codons. These are UAA, UAG, UGA present in the mrna, signals the termination of polypeptide synthesis and do not code for any known amino-acid. Q.No.9. Depict the chemical structure of cloverleaf model of trna.

6 trna from yeast. Fig. Cloverleaf structure of Q.No. 10. What is anti-codon and how it acts in protein synthesis? Ans. The terminal end of the anticodon arm contains the anticodon. An anticodon is a unit made up of three nucleotides, that correspond to the three bases of the codon on the mrna (Felsenfeld and Cantoni, 1964). Each trna contains a specific anticodon triplet sequence that can base-pair to one or more codons for an amino acid. For example, the codon for lysine is AAA; the anticodon of a lysine trna might be UUU. Some anticodons can pair with more than one codon due to a phenomenon known as wobble base pairing. In the genetic code, it is common for a single amino acid to be specified by all four third-position possibilities, or at least by both Pyrimidines and Purines; for example, the amino acid glycine is coded for by the codon sequences GGU, GGC, GGA, and GGG. Q.No.11. What is non-coding RNA? Ans. A non-coding RNA (ncrna) is a functional RNA molecule that is not translated into a protein. Lessfrequently used synonyms are non-protein-coding RNA (npcrna), non-messenger RNA (nmrna), small non-messenger RNA (snmrna) and functional RNA

7 (frna). The term small RNA (srna) is often used for small bacterial ncrnas. Q. No.12. What is sedimentation coefficient? Ans. Sedimentation coefficient is the time taken by any solid particle to settle or to sediment in the process of centrifugation. Q.No.13. Write down the chemical composition of ribosomes Ans. Ribosomes are tiny particles, about 200 A. It is composed of both proteins and RNA; in fact it has approximately 37-62% RNA, and rest are made up of proteins (Cohn and Norman, 1964). The RNA present in ribosomes are obviously called ribosomal RNA, and they are produced in the nucleolus. Q.No.14. How ribosomes help in protein synthesis? Ans. The ribosomes play a very important role in protein synthesis, which is the process by which proteins are made from the amino acids. Without the ribosomes the message would not be read, thus proteins could not be produced. The ribosomes are the primary agent in the process of translating the mrna into a specific amino acid chain, which consists of two subunits. These subunits are made up of ribosomal RNA (rrna), and together contain up to eighty-two specific proteins assembled in a precise sequence. This assembled ribosome displays a series of small groves, tunnels, and platforms, where the action of protein synthesis occurs. There are the active sites, each dedicated to one of the tasks required for translation of mrna into protein. Proteins being

8 synthesized for export out of the cell, are made by ribosomes attached to the rough endoplasmic reticulum. The process of protein synthesis begins with the capture of the trna, which is carrying an amino acid, by an initiation factor. This binds to a small ribosomal subunit, which occupies one of the active sites in the ribosomes, the P (protein) site. This initiation complex recognized and binds to the 5' end of an mrna molecule and slides down to the initiation codon, which is always an AUG sequence of amino acids. The large subunit of the ribosome now joins the complex, then the second aminoaceyl-trna attach with the A-site on this attached ribosome. The continued carrying of amino-acids by trnas to the ribosome leads to the formation of a long poly-peptide chain. After the complete synthesis of polypeptide chain the ribosome dissociates into its sub-units. Q. No. 15. What are polyribosomes? Ans. When many free ribosomes get attached with mrna in the process of translation, they form a chain along the length of mrna called polyribosomes or polysomes. The number of ribosomes associated in the polysomal chains depends on the size of the mrna. This is also associated with the size of the protein that is being synthesized.