Table of Contents
Overview of RNA
Ribonucleic acid (RNA) is a nucleic acid like DNA, but it plays different roles in the cell. While DNA serves mainly as long‑term storage of genetic information, RNA acts primarily as a working copy, adaptor, structural component, or catalyst in the processes that read and use genetic information.
In this chapter we focus on what is specific to RNA:
- its chemical and structural features,
- its main types and their functions,
- and some special functional RNAs.
General aspects of nucleic acids and the genetic code are treated in other chapters.
Chemical and Structural Features of RNA
Monomers: Ribonucleotides
RNA is a polymer of ribonucleotides. Each ribonucleotide has:
- a phosphate group,
- the sugar ribose,
- a nitrogenous base.
The bases in RNA are:
- purines: adenine (A), guanine (G),
- pyrimidines: cytosine (C), uracil (U).
Uracil (U) in RNA replaces thymine (T), which is typical of DNA.
The sugar ribose has an –OH group on the 2' carbon. This 2'-hydroxyl group is absent in deoxyribose of DNA (which has –H at 2'). This small difference has important consequences.
Primary Structure: Single-Stranded Polymer
RNA typically exists as a single strand. The backbone is made of alternating ribose and phosphate groups, connected by phosphodiester bonds between the 3' carbon of one sugar and the 5' carbon of the next.
Like DNA, RNA strands have direction:
- a free phosphate at the 5' end,
- a free hydroxyl at the 3' end.
Sequences are written from 5' to 3', for example: 5'-AUGCUUACG-3'.
Secondary and Tertiary Structures
Even though RNA is single-stranded, it can fold back and base pair with itself. Typical base pairs:
- A–U (two hydrogen bonds),
- G–C (three hydrogen bonds),
- plus some non‑standard pairs (e.g. G–U wobble pairs).
From these interactions, characteristic structural elements form:
- hairpins: short double-stranded stems with a single-stranded loop,
- internal loops and bulges: unpaired regions interrupting stems,
- multi‑branched junctions: where several stems meet.
When many such elements interact, RNA folds into a specific three-dimensional (tertiary) structure, essential for the function of many RNAs (e.g. tRNA, rRNA, ribozymes).
Consequences of the 2'-OH Group
The presence of the 2'-OH on ribose:
- makes RNA less chemically stable than DNA (more prone to hydrolysis),
- allows more flexibility in folding and more diverse 3D structures,
- enables catalytic activity in some RNAs (ribozymes), because the 2'-OH can directly participate in chemical reactions.
These properties fit RNA’s roles as a transient, versatile molecule rather than a long-term archive.
Main Classes of RNA in Gene Expression
The genetic code chapter explains how sequence information is translated into proteins. Here we focus on the specific RNAs involved.
Messenger RNA (mRNA)
mRNA carries the information copied from DNA to the ribosomes, where proteins are synthesized.
Key features:
- Origin: produced by transcription of protein‑coding genes.
- Sequence: contains codons (triplets of bases) that specify amino acids.
- Lifetime: generally short‑lived, allowing rapid adjustment of protein production.
In prokaryotes (bacteria and archaea):
- mRNAs are often polycistronic: one mRNA can contain the coding regions for several proteins, usually from the same operon.
- mRNA is usually not heavily processed: transcription and translation can occur simultaneously.
In eukaryotes:
- primary transcripts (pre‑mRNA) contain exons (coding) and introns (non‑coding).
- pre‑mRNA is processed in the nucleus to become mature mRNA:
- 5' cap: a modified guanine nucleotide added to the 5' end,
- splicing: introns removed, exons joined,
- 3' poly(A) tail: a stretch of adenine nucleotides added to the 3' end.
- mature mRNA is usually monocistronic: one mRNA encodes one main protein.
These processing steps influence mRNA stability, export from the nucleus, and translational efficiency.
Transfer RNA (tRNA)
tRNAs act as adaptors between codons in mRNA and amino acids during protein synthesis.
Key properties:
- Size: relatively short, about 70–90 nucleotides.
- Structure:
- cloverleaf secondary structure with:
- acceptor stem (3' end with the sequence CCA, where the amino acid is attached),
- anticodon loop (contains a three‑base anticodon),
- D loop and TψC loop (important for correct folding and recognition),
- L‑shaped tertiary structure in three dimensions.
- Function:
- each tRNA is “charged” with a specific amino acid by an aminoacyl‑tRNA synthetase (enzyme specificity links the correct amino acid to the correct tRNA),
- the anticodon base pairs with the complementary codon on mRNA during translation.
Because of the wobble position in codons and anticodons, fewer tRNA species are needed than there are codons.
Ribosomal RNA (rRNA)
rRNA is a major structural and functional component of ribosomes, the cellular machines that synthesize proteins.
Key aspects:
- Abundant: rRNA makes up the bulk of cellular RNA.
- Association with proteins: rRNAs combine with ribosomal proteins to form the large and small ribosomal subunits.
- Catalytic role:
- the ribosome’s active site for peptide bond formation is composed of rRNA; the ribosome is a ribozyme,
- rRNA positions mRNA and tRNAs correctly and catalyzes the joining of amino acids.
In prokaryotes:
- typical rRNAs are 23S, 16S, and 5S rRNA.
In eukaryotes:
- typical rRNAs are 28S, 18S, 5.8S, and 5S rRNA.
The “S” (Svedberg unit) relates to sedimentation behavior in a centrifuge, which reflects size and shape, not simply length.
Regulatory and Processing RNAs
Beyond the “classic” mRNA, tRNA, and rRNA, many RNAs regulate gene activity, modify other RNAs, or participate in RNA processing.
Small Nuclear RNA (snRNA)
snRNAs are found in the nucleus of eukaryotic cells and are essential for RNA processing.
Main roles:
- core components of the spliceosome, the complex that removes introns from pre‑mRNA,
- recognize splice sites and catalyze the splicing reactions,
- often base pair with pre‑mRNA and with each other, forming small nuclear ribonucleoproteins (snRNPs) together with proteins.
snRNAs are crucial for generating correctly spliced, mature mRNAs.
Small Nucleolar RNA (snoRNA)
snoRNAs mainly function in the nucleolus of eukaryotic cells, a region involved in ribosome production.
Functions:
- guide chemical modifications of rRNA (and some tRNAs and snRNAs), such as:
- 2'-O‑methylation of ribose,
- conversion of uridine to pseudouridine,
- work as guide RNAs: specific base pairing directs modifying enzymes to precise nucleotide positions.
These modifications help rRNAs fold correctly and function efficiently within ribosomes.
MicroRNA (miRNA) and Small Interfering RNA (siRNA)
miRNAs and siRNAs are short regulatory RNAs (typically about 20–25 nucleotides) that influence gene expression by interacting with mRNA.
microRNA (miRNA)
miRNAs are encoded by the genome and produced via a multi‑step processing pathway.
Characteristics and actions:
- derived from longer primary transcripts (pri‑miRNAs),
- processed in the nucleus and cytoplasm into short double‑stranded RNA; one strand becomes the mature miRNA,
- loaded into a protein complex (RISC: RNA‑induced silencing complex),
- base pairs with target mRNAs, usually imperfectly in animals, more precisely in plants,
- can:
- block translation,
- or trigger degradation of the target mRNA.
miRNAs are important regulators of development, cell differentiation, and many physiological processes.
Small Interfering RNA (siRNA)
siRNAs often arise from double‑stranded RNA of external or internal origin (e.g. viruses, transposons, or experimental introduction).
Properties:
- generated by cleavage of double-stranded RNA into short fragments,
- also loaded into RISC complexes,
- usually show nearly perfect complementarity to their target mRNAs,
- typically induce cleavage and degradation of the bound mRNA.
siRNA pathways are central to antiviral defense in many organisms and are widely used as experimental tools to silence genes.
Long Non‑Coding RNA (lncRNA)
Long non‑coding RNAs are RNA molecules longer than about 200 nucleotides that are not translated into proteins.
Their functions are diverse and often still under investigation, but known roles include:
- scaffolding: bringing together proteins into complexes,
- guiding: recruiting chromatin‑modifying enzymes to specific genomic regions,
- decoying: binding and sequestering proteins or other RNAs,
- affecting transcription, splicing, and chromatin structure.
lncRNAs expand the regulatory potential of the genome far beyond protein‑coding sequences.
Catalytic RNA: Ribozymes
Some RNA molecules can catalyze chemical reactions; these are called ribozymes.
Examples:
- self‑splicing introns: intron RNAs that can cut themselves out of RNA transcripts,
- the peptidyl transferase center of the ribosome: rRNA catalyzes peptide bond formation,
- small synthetic ribozymes that can be designed in the laboratory to catalyze specific reactions.
Key features:
- catalytic activity depends on the specific 3D folding of the RNA,
- catalysis often involves:
- precise positioning of substrates,
- participation of functional groups (including 2'-OH),
- assistance from metal ions (e.g. Mg²⁺).
Ribozymes support the idea that RNA can act both as genetic material and as catalyst, a concept important for hypotheses about the early evolution of life (discussed elsewhere under the “RNA world”).
RNA in Viruses
Some viruses use RNA instead of DNA as their genetic material.
Main types:
- single-stranded RNA viruses:
- positive‑sense (+) RNA genomes: RNA can serve directly as mRNA for protein synthesis,
- negative‑sense (−) RNA genomes: RNA is complementary to mRNA and must be copied into (+) RNA by a viral RNA‑dependent RNA polymerase.
- double-stranded RNA viruses: genomes consist of base‑paired RNA segments.
Retroviruses (a special group of RNA viruses) use RNA genomes but replicate through a DNA intermediate made by reverse transcriptase; details of this reversal of the usual information flow are covered in the chapter on retroviruses.
These viral strategies illustrate the versatility of RNA as an information carrier.
Stability and Turnover of RNA
RNA molecules vary greatly in their stability:
- rRNA and tRNA: relatively long‑lived because they are structural and catalytic components that are reused.
- mRNA: often short‑lived, allowing the cell to quickly adjust which proteins are produced and in what amounts.
- many regulatory RNAs: can have tightly controlled synthesis and degradation, so regulation can be rapid and reversible.
Cells possess RNases (ribonucleases), enzymes that degrade RNA. Controlled RNA turnover is an important layer of gene regulation, determining how long a given message or regulatory signal persists.
Summary
RNA is a chemically distinct and functionally highly versatile nucleic acid. Its 2'-OH group and single-stranded nature allow complex folding, catalysis, and diverse interactions with DNA, proteins, and other RNAs. Different classes of RNA—mRNA, tRNA, rRNA, and numerous non‑coding RNAs—form an integrated network that reads, interprets, and regulates the genetic information stored in DNA.