Fundamentals of Molecular Biology. Part 2: Molecular Genetic Mechanisms - A. N. Ogurtsov 2011

Basic Molecular Genetic Mechanisms
RNA Conformations

The Introduction/19.html">Primary Structure of RNA is similar to that of DNA, but RNA possesses two key differences:

1) the presence of a hydroxyl group on the ribose at the 2' position (Figure 6),

2) the nucleic acid base uracil instead of thymine found in DNA.

The hydroxyl group in ribose makes RNA more chemically labile (reactive) compared to DNA and provides the OH group required in RNA-catalyzed reactions. As a result of this lability, RNA, unlike DNA, is degraded into mononucleotides in an alkaline solution.

Class="center">

Figure 6 - Pentoses of Ribonucleic Acids: a - ribose; b - deoxyribose

Much like DNA, RNA is a polynucleotide that can form a single helix, a double helix, or adopt linear or circular Conformations.

Hybrid RNA-DNA Double helices are also possible.

Unlike DNA, most cellular RNA is single-stranded, with various Secondary structure elements (Figure 7) that enable it to perform specific Functions.

Figure 7 - Elements of RNA secondary structure: a - hairpin; b - loop; c - pseudoknot

Simple secondary structures are formed, just as in DNA, through complementary base pairing.

Hairpins are formed by the base pairing of RNA segments separated by 5–10 NUCLEOTIDES. When the distance between the pairing segments exceeds 10 nucleotides (up to 100), these structures are referred to as stem-loops. These simple motifs can interact to form more complex tertiary structures, one of which is known as a pseudoknot.

Thus, base pairing is the fundamental process that dictates the Functional Properties of both DNA and RNA.

Below, we will examine in detail the secondary and tertiary Structural Features of tRNA, rRNA, and mRNA, which account for their functional differences and interactions during METABOLISM/35.html">Protein Biosynthesis.

It should be noted that RNA molecules, similarly to Proteins, exhibit a domain architecture. More structured and rigid domains are interconnected by less structured (and more flexible) regions.

The domain structure of RNA is not merely an analogue of alpha- and beta-structures in protein molecules. In some cases, this domain Organization confers catalytic activity upon the RNA. Such catalytic RNAs are called ribozymes. Although ribozymes typically associate with proteins that stabilize their structure, it is the RNA molecule itself that acts as the catalyst.

Certain ribozymes catalyze RNA splicing, a process in which specific internal segments of RNA are excised and removed, and the remaining RNA fragments are joined into a continuous strand. This process occurs during The formation of most functional mRNAs in Eukaryotic Cells and has also been discovered in prokaryotes. Notably, some RNA molecules are capable of self-splicing.

Ribosomal rRNAs perform a catalytic function in the formation of peptide bonds during Protein Synthesis.

Conclusions

DNA serves as the repository of Genetic information that dictates the Amino Acid Sequence of proteins. This information is transcribed into several types of RNA—including messenger mRNA, transfer tRNA, and ribosomal rRNA—which carry out protein synthesis.

DNA and Raman are long, unbranched polymers of nucleotides composed of a phosphorylated pentose linked to an organic base, which is either a purine or a pyrimidine.

The Purines adenine and guanine, and the pyrimidine cytosine, are found in both DNA and RNA. The pyrimidine thymine, present in DNA, is replaced by the pyrimidine uracil in RNA.

Adjacent nucleotides in Nucleic Acids are linked by phosphodiester bonds. The polynucleotide chain has a chemical polarity: a 5' end with a free phosphate group attached to the 5' carbon of the pentose, and a 3' end with a free hydroxyl group attached to the 3' carbon of the pentose.

Native DNA (B-form) consists of two complementary, antiparallel polynucleotide chains wound into a double helix, with the nucleic acid bases on the inside and the two sugar-phosphate backbones on the outside. Hydrogen Bonds between complementary Base Pairs across the polynucleotide chains and hydrophobic interactions between adjacent nucleic acid bases within the same chain stabilize this structure.

Bases in nucleic acids interact to form hydrogen bonds. The standard Watson-Crick base pairs are G=C, A=T (in DNA), and A=U (in RNA). Base pairing stabilizes the three-dimensional structure of DNA and RNA.

Protein binding to DNA can distort The Double Helix structure, causing local bending and unwinding of the DNA molecule.

Heating unwinds the DNA double helix into two single strands (Denaturation). The melting Temperature of DNA, Tm, increases with a higher concentration of G=C pairs. Under favorable conditions, individual complementary polynucleotide strands renature.

Circular DNA molecules can twist to form a supercoiled structure. Topoisomerase Enzymes relieve torsional stress and eliminate DNA Supercoiling.

Cellular RNAs are single-stranded polynucleotides, some of which possess well-defined secondary and tertiary structures. Certain RNAs, known as ribozymes, exhibit catalytic activity.

Self-Assessment Questions

1. List and describe the four main genetic processes.

2. Describe the Three Functions of RNA in protein biosynthesis.

3. State the Central dogma of molecular biology.

4. What deviations from the central dogma of molecular biology are you aware of?

5. Which property of DNA allows it to bend easily when complexed with proteins?

6. What is meant by DNA denaturation?

7. What is defined as the melting temperature of DNA?

8. How does A change in pH affect the melting temperature of DNA?

9. Why does changing the ion concentration in solution alter the melting temperature of DNA?

10. What is DNA renaturation, and what processes promote renaturation?

11. What is DNA supercoiling?

12. What are the Similarities and differences between the functions of topoisomerase I and topoisomerase II?

13. What is the function of the DNA gyrase enzyme?

14. What elements of RNA secondary structure do you know?

15. What are ribozymes?