RNA- Properties, Structure, Types and Functions

RNA, or ribonucleic acid, is a type of nucleic acid that plays a vital role in the expression of genetic information. RNA is similar to DNA, or deoxyribonucleic acid, in that it is composed of nucleotides, which are the building blocks of nucleic acids. However, RNA differs from DNA in several aspects, such as its structure, composition, and function.

Structure of RNA

The basic structure of RNA is a single-stranded helix, which means that it has only one strand of nucleotides that forms a twisted shape. Unlike DNA, which has two complementary strands that form a double helix, RNA can fold back on itself and form base pairs within the same strand. This creates regions of double-strandedness and complex shapes in some RNA molecules.

Each nucleotide in RNA consists of three components: a nitrogenous base, a pentose sugar, and a phosphate group. The nitrogenous bases in RNA are adenine (A), guanine (G), cytosine (C), and uracil (U). Uracil replaces thymine (T), which is found in DNA, as the complementary base to adenine. The pentose sugar in RNA is ribose, which has an extra hydroxyl group compared to deoxyribose in DNA. The phosphate group connects the sugar of one nucleotide to the sugar of the next nucleotide, forming a backbone for the RNA strand.

The nucleotides in RNA are linked by 3′ –> 5′ phosphodiester bonds, which means that the 3′ hydroxyl group of one nucleotide is attached to the 5′ phosphate group of another nucleotide. This creates a polarity for the RNA strand, which has a free 5′ phosphate group at one end and a free 3′ hydroxyl group at the other end. The directionality of the RNA strand is important for its interaction with other molecules, such as proteins and enzymes.

The sequence of nucleotides in RNA determines its function and specificity. Different regions of the RNA strand can have different roles and interactions depending on their base composition and structure. For example, some RNA molecules have a 5′ cap and a 3′ poly-A tail that protect them from degradation and facilitate their transport and recognition. Some RNA molecules have a codon region that encodes for amino acids and a non-coding region that regulates their expression. Some RNA molecules have an anticodon region that matches with a codon region and an amino acid attachment site that carries an amino acid.

The structure of RNA is dynamic and flexible, allowing it to adopt various conformations and perform diverse functions. Some RNA molecules can act as catalysts, sensors, regulators, or messengers in various biological processes. The diversity and versatility of RNA make it an essential molecule for life.

RNA and DNA are both nucleic acids that store and transmit genetic information. However, they have several structural and functional differences that make them suitable for different roles in the cell. Here are some of the main differences between RNA and DNA:

• Sugar: RNA has a ribose sugar in its backbone, while DNA has a deoxyribose sugar. The ribose sugar has an extra hydroxyl group (-OH) at the 2` position of the ring, which makes RNA more reactive and less stable than DNA.
• Bases: RNA has four nitrogenous bases: adenine (A), guanine (G), cytosine (C), and uracil (U). DNA has the same bases except for thymine (T), which replaces uracil in DNA. Uracil can form base pairs with adenine, just like thymine, but it is more prone to chemical modifications and mutations.
• Strands: RNA is usually single-stranded, meaning it has only one strand of nucleotides. DNA is usually double-stranded, meaning it has two complementary strands of nucleotides that are held together by hydrogen bonds between the bases. The double-stranded structure of DNA gives it more stability and protection from damage.
• Shape: RNA can fold into various shapes and forms due to its single-stranded nature and the presence of unusual bases. Some of these shapes include loops, hairpins, stems, and pseudoknots. These shapes allow RNA to perform diverse functions such as catalysis, regulation, and sensing. DNA has a fixed shape of a double helix, which is twisted into a right-handed direction. The double helix allows DNA to store large amounts of information in a compact way and to replicate accurately.
• Location: RNA is mainly found in the cytoplasm of the cell, where it performs various tasks such as protein synthesis, gene expression, and signal transduction. Some RNA molecules are also found in the nucleus, where they are involved in transcription, splicing, and editing. DNA is mainly found in the nucleus of the cell, where it is organized into chromosomes that contain the genetic blueprint of the organism. Some DNA molecules are also found in the mitochondria and chloroplasts of eukaryotic cells, where they encode some essential genes for cellular respiration and photosynthesis.

• Function: RNA has multiple functions in the cell, depending on its type and structure. Some of the main functions of RNA are:

  • Messenger RNA (mRNA): carries the genetic code from DNA to the ribosomes, where it is translated into proteins.
  • Ribosomal RNA (rRNA): forms part of the ribosomes, where it helps to assemble amino acids into polypeptide chains.
  • Transfer RNA (tRNA): transports amino acids to the ribosomes, where it recognizes the codons on mRNA and adds the corresponding amino acids to the growing polypeptide chain.
  • Other types of RNA: such as microRNA (miRNA), small interfering RNA (siRNA), long non-coding RNA (lncRNA), etc., have various roles in regulating gene expression, silencing genes, modifying RNAs, and responding to cellular signals.

DNA has one main function in the cell: to store and transmit genetic information. DNA contains the instructions for all the traits and characteristics of an organism. It also replicates itself during cell division to pass on its information to the daughter cells.

RNA secondary structure

Unlike DNA, which is usually double-stranded and forms a stable double helix, RNA is mostly single-stranded and can fold back on itself to form various shapes and structures. This is called RNA secondary structure, and it is determined by the complementary base pairing between different regions of the RNA strand. For example, if a segment of RNA has the sequence AUUCCGA, it can form a hairpin loop by pairing the A with the U, the U with the A, and the C with the G, leaving the central C unpaired. The hairpin loop is one of the most common motifs in RNA secondary structure, and it can have various functions depending on the context.

RNA secondary structure can also involve more complex interactions, such as base stacking, bulges, internal loops, pseudoknots, and long-range interactions. Base stacking refers to the tendency of adjacent bases to align in a way that stabilizes the structure and affects its shape. Bulges and internal loops are regions where one or both strands have unpaired nucleotides that disrupt the regular pairing pattern. Pseudoknots are structures where a loop in one part of the RNA pairs with a segment outside the loop, forming a knot-like shape. Long-range interactions are base pairings that occur between distant regions of the RNA strand, often spanning hundreds or thousands of nucleotides.

RNA secondary structure is important for many biological processes and functions. For example, RNA secondary structure can affect the stability, folding, and degradation of RNA molecules in the cell. It can also influence the transcription, splicing, translation, and regulation of gene expression by creating or blocking access to certain sequences or binding sites. Moreover, RNA secondary structure can enable some RNA molecules to act as catalysts or sensors by changing their shape in response to external stimuli or internal signals.

Some examples of RNA molecules that have significant secondary structure are:

• Ribosomal RNA (rRNA), which forms the core of the ribosome and participates in protein synthesis.
• Transfer RNA (tRNA), which has a cloverleaf structure with four loops and carries amino acids to the ribosome.
• Messenger RNA (mRNA), which can have secondary structures that affect its translation efficiency, stability, and interactions with other molecules.
• MicroRNA (miRNA) and small interfering RNA (siRNA), which are short RNAs that regulate gene expression by binding to complementary sequences on target mRNAs and causing their degradation or repression.
• Ribozymes, which are RNA molecules that can catalyze chemical reactions such as cleavage, ligation, or modification of other RNAs. Examples include ribonuclease P (RNase P), which processes precursor tRNAs; hammerhead ribozyme, which cleaves itself and other RNAs; and spliceosome, which removes introns from pre-mRNAs.

In summary, RNA secondary structure is the result of complementary base pairing between different regions of a single-stranded RNA molecule. It can create various shapes and structures that have important roles in many biological processes and functions.

In both prokaryotes and eukaryotes, there are three main types of RNA – rRNA (ribosomal), tRNA (transfer), and mRNA (messenger). Each type of RNA has a different structure and function in the cell.

• rRNA (ribosomal): Found in the ribosomes and account for 80% of the total RNA present in the cell. Ribosomes consist of two major components: the small ribosomal subunits, which read the mRNA, and the large subunits, which join amino acids to form a polypeptide chain. Each subunit comprises one or more rRNA molecules and a variety of ribosomal proteins. rRNA directs the translation of mRNA into proteins by binding to tRNAs and other molecules that are crucial for protein synthesis.

• tRNA (transfer): tRNA is the smallest of the 3 types of RNA having about 75-95 nucleotides. tRNAs are an essential component of translation, where their main function is the transfer of amino acids during protein synthesis. Therefore they are called transfer RNAs. Each of the 20 amino acids has a specific tRNA that binds with it and transfers it to the growing polypeptide chain. tRNAs also act as adapters in the translation of the genetic sequence of mRNA into proteins. Therefore they are also called adapter molecules. tRNAs have a clover leaf structure which is stabilized by strong hydrogen bonds between the nucleotides. Apart from the usual 4 bases, they normally contain some unusual bases mostly formed by methylation of the usual bases, for example, methyl guanine and methylcytosine. Three structural loops are formed via hydrogen bonding. The 3′ end serves as the amino acid attachment site. The center loop encompasses the anticodon. The anticodon is a three-base nucleotide sequence that binds to the mRNA codon. This interaction between codon and anticodon specifies the next amino acid to be added during protein synthesis.

• mRNA (messenger): Accounts for about 5% of the total RNA in the cell. Most heterogeneous of the 3 types of RNA in terms of both base sequence and size. It carries the genetic code copied from the DNA during transcription in the form of triplets of nucleotides called codons. As part of post-transcriptional processing in eukaryotes, the 5’ end of mRNA is capped with a guanosine triphosphate nucleotide, which helps in mRNA recognition during translation or protein synthesis. Similarly, the 3’ end of an mRNA has a poly A tail or multiple adenylate residues added to it, which prevent enzymatic degradation of mRNA. Both 5’ and 3’ end of an mRNA imparts stability to the mRNA. mRNA transcribes the genetic code from DNA into a form that can be read and used to make proteins. mRNA carries genetic information from the nucleus to the cytoplasm of a cell.

Messenger RNA (mRNA) is a type of RNA that carries the genetic code copied from the DNA during transcription in the form of triplets of nucleotides called codons. Each codon specifies a particular amino acid that will be incorporated into the protein. mRNA accounts for about 5% of the total RNA in the cell and is the most heterogeneous of the three types of RNA in terms of both base sequence and size.

As part of post-transcriptional processing in eukaryotes, the 5′ end of mRNA is capped with a guanosine triphosphate nucleotide, which helps in mRNA recognition during translation or protein synthesis. Similarly, the 3′ end of an mRNA has a poly A tail or multiple adenylate residues added to it, which prevent enzymatic degradation of mRNA. Both 5′ and 3′ end of an mRNA impart stability to the mRNA.

The function of mRNA is to transcribe the genetic code from DNA into a form that can be read and used to make proteins. mRNA carries genetic information from the nucleus to the cytoplasm of a cell, where it binds to ribosomes and serves as a template for protein synthesis. The ribosomes read the codons on the mRNA and match them with the corresponding anticodons on the transfer RNA (tRNA) molecules that carry amino acids. The amino acids are then joined together by peptide bonds to form a polypeptide chain, which is later folded and modified to form a functional protein.

mRNA plays a crucial role in gene expression, as it determines which genes are turned on or off in response to various signals and stimuli. The regulation of mRNA synthesis, processing, transport, stability, and translation can affect the amount and type of proteins produced by a cell. Some examples of how mRNA can be regulated are:

• Alternative splicing: A process in which different segments of an mRNA transcript are joined together in different ways to produce different variants of proteins from the same gene.
• RNA editing: A process in which some nucleotides in an mRNA transcript are modified after transcription, resulting in changes in the amino acid sequence of the protein.
• RNA interference: A process in which small RNA molecules (such as microRNAs or siRNAs) bind to complementary sequences on an mRNA transcript and either block its translation or induce its degradation.
• Translational control: A process in which various factors affect the initiation, elongation, or termination of protein synthesis by interacting with the mRNA or the ribosome.

mRNA is also involved in some cellular processes that do not involve protein synthesis, such as:

• Reverse transcription: A process in which an enzyme called reverse transcriptase uses an mRNA template to synthesize a complementary DNA strand, which can then be integrated into the genome or used for other purposes.
• RNA vaccines: A type of vaccine that uses synthetic mRNA molecules that encode antigens (such as viral proteins) to elicit an immune response in the host. The mRNA is delivered into the cells by lipid nanoparticles or other methods and translated into proteins that stimulate the production of antibodies and T cells.

mRNA is a versatile and dynamic molecule that mediates the flow of genetic information from DNA to proteins and influences various cellular functions and responses. By understanding how mRNA works and how it can be manipulated, scientists can explore new ways of studying gene expression, developing therapeutics, and creating novel biotechnologies.

Ribosomal RNA (rRNA) is the most abundant type of RNA in the cell, accounting for about 80% of the total RNA. It is found in the ribosomes, which are the molecular machines that synthesize proteins from mRNA. Ribosomes consist of two major components: the small ribosomal subunit, which reads the mRNA, and the large ribosomal subunit, which joins amino acids to form a polypeptide chain. Each subunit comprises one or more rRNA molecules and a variety of ribosomal proteins.

The rRNA molecules have different sizes and functions depending on their location in the ribosome. The small rRNA (also called 16S rRNA in prokaryotes and 18S rRNA in eukaryotes) forms the core of the small subunit and binds to the mRNA. It also contains a region called the anti-Shine-Dalgarno sequence, which recognizes a complementary sequence on the mRNA called the Shine-Dalgarno sequence. This interaction ensures that the ribosome starts translating at the correct position on the mRNA.

The large rRNA (also called 23S rRNA in prokaryotes and 28S rRNA in eukaryotes) forms the core of the large subunit and catalyzes the formation of peptide bonds between amino acids. It also contains a region called the peptidyl transferase center, which is where the peptide bond formation occurs. The large rRNA is thus considered a ribozyme, an RNA molecule that acts as an enzyme.

In addition to the small and large rRNAs, there are also other rRNAs that are associated with either subunit. For example, in prokaryotes, there is a 5S rRNA that binds to the large subunit and helps stabilize its structure. In eukaryotes, there are three additional rRNAs: 5S rRNA, 5.8S rRNA, and 5.8S rRNA. These rRNAs form a complex with the large rRNA and some ribosomal proteins and are collectively called the 5S/5.8S complex.

The function of rRNA is to direct the translation of mRNA into proteins. It does so by providing a scaffold for the assembly of ribosomal proteins and by facilitating the interactions between mRNA, tRNA, and ribosomal proteins. It also plays an active role in catalyzing peptide bond formation and ensuring the fidelity of translation. Without rRNA, protein synthesis would not be possible.

tRNA is the smallest of the 3 types of RNA having about 75-95 nucleotides. tRNAs are an essential component of translation, where their main function is the transfer of amino acids during protein synthesis. Therefore they are called transfer RNAs.

Each of the 20 amino acids has a specific tRNA that binds with it and transfers it to the growing polypeptide chain. tRNAs also act as adapters in the translation of the genetic sequence of mRNA into proteins. Therefore they are also called adapter molecules.

Structure of tRNA

tRNAs have a clover leaf structure which is stabilized by strong hydrogen bonds between the nucleotides. Apart from the usual 4 bases, they normally contain some unusual bases mostly formed by methylation of the usual bases, for example, methyl guanine and methylcytosine.

Three structural loops are formed via hydrogen bonding.

• The 3′ end serves as the amino acid attachment site.
• The center loop encompasses the anticodon.
• The anticodon is a three-base nucleotide sequence that binds to the mRNA codon.
• This interaction between codon and anticodon specifies the next amino acid to be added during protein synthesis.

The clover leaf structure of tRNA folds further into an L-shaped three-dimensional structure that fits into the ribosome.

Function of tRNA

Transfer RNA brings or transfers amino acids to the ribosome that correspond to each three-nucleotide codon of rRNA. The amino acids then can be joined together and processed to make polypeptides and proteins.

The process of tRNA-mediated protein synthesis involves the following steps:

• Activation of amino acids: Each amino acid is activated by a specific enzyme called aminoacyl-tRNA synthetase that attaches it to its corresponding tRNA molecule. This requires energy in the form of ATP. The resulting complex is called an aminoacyl-tRNA or a charged tRNA.
• Initiation of translation: The initiation complex consists of a small ribosomal subunit, an mRNA molecule, and an initiator tRNA carrying methionine. The initiator tRNA recognizes the start codon (AUG) on the mRNA and binds to it.
• Elongation of polypeptide chain: The large ribosomal subunit joins the initiation complex and forms two sites for tRNA binding: the A site (aminoacyl) and the P site (peptidyl). The A site accepts a new charged tRNA that matches the next codon on the mRNA. The P site holds the growing polypeptide chain attached to a tRNA. A peptide bond is formed between the amino acids in the A and P sites, and the polypeptide chain is transferred to the A site. The uncharged tRNA in the P site is released and recycled. The ribosome moves one codon along the mRNA, bringing a new codon to the A site and repeating the cycle.
• Termination of translation: When a stop codon (UAA, UAG, or UGA) is reached on the mRNA, no corresponding tRNA can bind to it. Instead, a release factor binds to the stop codon and triggers the release of the polypeptide chain from the tRNA in the P site. The ribosome dissociates into its subunits and the mRNA is freed.

Besides the three main types of RNA, there are many other kinds of RNA molecules that have different properties and functions. Some examples are:

• MicroRNAs (miRNAs): These are small (~22 nucleotides) RNAs that regulate gene expression by binding to complementary sequences on mRNA and inhibiting translation or causing degradation of the target mRNA.
• Small interfering RNAs (siRNAs): These are similar to miRNAs but are derived from longer double-stranded RNAs that are processed by an enzyme called Dicer. They can also silence gene expression by targeting specific mRNAs for degradation or blocking translation.
• Long noncoding RNAs (lncRNAs): These are RNAs that are longer than 200 nucleotides and do not code for proteins. They have diverse roles in chromatin remodeling, transcriptional regulation, splicing, and RNA stability.
• Ribozymes: These are RNA molecules that can catalyze chemical reactions, such as cutting and joining other RNA molecules. They are found in some viruses, bacteria, and eukaryotes. One example is the ribosome, which is composed of rRNA and proteins and catalyzes peptide bond formation during protein synthesis .

Some other properties of RNA that distinguish it from DNA are:

• RNA is more reactive than DNA because it has a hydroxyl group on the 2` carbon of the ribose sugar, which makes it more prone to hydrolysis and base deamination .
• RNA has larger helical grooves than DNA, which makes it more accessible to enzymes and other molecules that can attack or modify it .
• RNA strands are continually made, broken down, and reused in the cell, unlike DNA strands that are mostly stable and conserved .
• RNA is more resistant to damage from UV light than DNA because it has uracil instead of thymine, which does not form thymine dimers that distort the DNA structure .
• RNA has a higher mutation rate than DNA because it lacks a proofreading mechanism during transcription and because some RNA viruses use an error-prone enzyme called reverse transcriptase to copy their RNA genome into DNA .

• RNA can have unusual bases that are modified by methylation or other chemical groups. These modifications can affect the stability, structure, and function of RNA molecules .

  Functions of RNA

RNA is a nucleic acid that has various roles in cellular processes, especially in protein synthesis. RNA can also serve as the genetic material for some viruses and as a catalyst for biological reactions. Here are some of the main functions of RNA:

• Coding: RNA carries the genetic information from DNA to the ribosomes, where it is translated into proteins. Messenger RNA (mRNA) is the type of RNA that encodes the amino acid sequence of a protein. Each mRNA molecule contains a series of codons, which are three-nucleotide sequences that specify a certain amino acid or a stop signal. The genetic code is universal and shared by all living organisms.

• Decoding: RNA helps to decode the mRNA sequence into a polypeptide chain. Transfer RNA (tRNA) is the type of RNA that carries an amino acid to the ribosome and recognizes the corresponding codon on the mRNA. Each tRNA molecule has an anticodon, which is a three-nucleotide sequence that is complementary to a specific codon. The tRNA also has an attachment site for the amino acid that matches the codon. The ribosome facilitates the base pairing between the codon and the anticodon and catalyzes the formation of a peptide bond between the amino acids.

• Regulation: RNA can regulate gene expression at various levels, such as transcription, splicing, translation, and degradation. Some RNA molecules can bind to DNA or RNA and affect their activity. For example, microRNA (miRNA) and small interfering RNA (siRNA) are small non-coding RNAs that can bind to complementary sequences on mRNA and inhibit its translation or cause its degradation. Riboswitches are segments of mRNA that can fold into different shapes and control gene expression in response to environmental signals.

• Expression: RNA can act as an enzyme and catalyze biological reactions. These RNA molecules are called ribozymes and can perform functions such as cutting and joining other RNA molecules, synthesizing new nucleotides, and modifying existing ones. For example, ribonuclease P (RNase P) is a ribozyme that cleaves the 5` end of precursor tRNA molecules to generate mature tRNAs. The ribosome itself is a large ribozyme that synthesizes proteins.

• Genetics: RNA can serve as the hereditary material for some viruses, such as retroviruses and coronaviruses. These viruses have RNA genomes that can be either single-stranded or double-stranded, positive-sense or negative-sense, linear or circular. Some RNA viruses can also integrate their genomes into the host DNA using reverse transcriptase, an enzyme that converts RNA into DNA. For example, human immunodeficiency virus (HIV) is a retrovirus that inserts its DNA copy into the human genome and causes acquired immunodeficiency syndrome (AIDS).

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