RNA Types and Structure

Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). While DNA stores the genetic information, RNA generally carries out the instructions encoded in the DNA but RNA also executes diverse non-coding functions. There are 3 major types of RNA that perform different but collaborative roles in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). During transcription, RNA is synthesized from DNA through a series of steps catalyzed by the enzyme RNA polymerase. The mRNA formed will serve as an amino acid template for protein synthesis. Translation proceeds with the tRNA transporting the corresponding amino acid based on the deciphered nucleotide sequence (codon) in the mRNA. The ribosomes, which are composed of rRNA, then facilitate the assembly of amino acids into a polypeptide. These components work together to convert the mRNA template obtained from DNA into the desired protein.

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General Features of RNA


Ribonucleic acid (RNA) is a single-stranded polymer of nucleotides that are linked through 3’–5’ phosphodiester bonds.

Nucleotides are the basic unit of any nucleic acid. The nucleotides in RNA are formed by the following parts:

  1. Ribose (sugar): Carbon 2’ is bonded to hydroxyl (OH)
    Note: In deoxyribonucleic acid (DNA), the word deoxyribose means that there is no oxygen (O) attached to carbon 2’.
  2. Phosphate group: bonded to the carbon 5’ of ribose; links to the OH of the carbon 3’ of the next nucleotide, forming a phosphodiester bond
  3. Nitrogenous base: bonded to the carbon 1’ of ribose
    • Purine bases:
      • Adenine
      • Guanine
    • Pyrimidine bases:
      • Cytosine
      • Uracil (Note: Uracil differs from DNA, which has thymine.)

Nucleic acid components:

  • Nucleobase: nitrogenous base (adenine)
  • Nucleoside: nitrogenous base + sugar (adenosine)
  • Nucleotide: nitrogenous base + sugar + phosphate (adenosine monophosphate)
  • Nucleic acid: polymer of nucleotide (RNA)
Table: RNA versus DNA
Sugar moietyRiboseDeoxyribose
Nitrogenous bases
  • Adenine
  • Guanine
  • Cytosine
  • Uracil (instead of thymine)
  • Adenine
  • Guanine
  • Cytosine
  • Thymine
Basic structureSingle strandedDouble stranded


  • Protein synthesis (messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA))
  • Gene expression regulation (micro RNA (miRNA), small regulatory RNA (sRNA), small interfering RNA (siRNA))
  • Processing of other RNAs (small nuclear RNA (snRNA), small nucleolar RNA (snoRNA))
  • Catalysis or metabolic function (ribozymes)
  • Genetic material in some viruses
  • Genome defense (siRNA (RNA interference), PIWI-interacting RNA (piRNA) in eukaryotes, CRISPR in prokaryotes)

Coding versus non-coding RNA

  • Coding RNA (translated into protein) such as:
    • mRNA
    • RNA of the viral genome
  • Non-coding RNA (other roles in the cell) such as:
    • tRNA
    • rRNA
    • miRNA
    • snoRNA
    • snRNA

Messenger RNA (mRNA)


  • Coding DNA sequence (CDS):
    • Broken into 3 base sequences known as codons (see mnemonic); correspond to specific amino acids
    • Begins with an initiation codon (AUG)
    • Ends with a termination codon (UGA, UAA, and UAG)
  • Untranslated region (UTR) or non-coding sequences (see differences below):
    • 5’ cap
    • 3’ poly-A tail
    • Shine-Dalgarno sequence (in prokaryotes)


To remember mRNA start codons, use the mnemonic AUG:

  • InAUGurates protein synthesis 
  • Are U Going

To remember mRNA stop codons, use the mnemonics UGA, UAA, and UAG:

  • U Go Away
  • U Are Away
  • U Are Gone
Transcription process and synthesis of mRNA

Illustration of transcription process and synthesis of mRNA

Image by Lecturio.


Messenger RNA (mRNA) serves as an amino acid template for protein synthesis.

  • During transcription, mRNA has the following characteristics:
    • Complementary to the antisense or template strand (facilitated by the enzyme RNA polymerase)
    • Becomes a copy of the coding strand (sense strand)
  • Messenger RNA is synthesized from the 5’ end to the 3’ end (because RNA polymerase can only add nucleotides to the 3’ end of the mRNA chain).
  • The initial transcript is known as heterogeneous nuclear RNA (hnRNA).
  • Processed hnRNA, which has the addition of the 5’ cap and the 3’ poly-A tail followed by splicing, becomes mRNA.

Prokaryotic versus eukaryotic mRNA

Prokaryotic mRNA

  • Polycistronic: 
    • One mRNA = several polypeptides 
    • In bacteria, clusters of related genes or operons are transcribed together in a single mRNA.
  • The CDS is translated into proteins immediately after being synthesized (no post-transcriptional modifications).
  • The 5’ UTR contains a Shine-Dalgarno sequence that helps recruit the ribosome to mRNA for protein synthesis.

Eukaryotic mRNA

  • Monocistronic: 
    • One mRNA = single polypeptide 
    • One initiation and termination codon producing one polypeptide chain
  • Modified extensively before being translated into proteins:
    • Capping of 5’ end: linkage of 7-methylguanosine 
      • Aids in recognition by the protein synthesis machinery 
      • Protects from degradation by exonucleases
    • The CDS undergoes modification or splicing of introns (non-coding segments).
    • Addition of the 3’ poly-A tail: chain of adenylate molecules (maintains the stability of mRNA as it exits the nucleus into the cytosol)

There is a long-held belief that prokaryotes lack the 5’ cap. Recently, however, some bacteria have been found to have a 5’ nicotinamide adenine dinucleotide (NAD) cap:

  • Appears to protect bacterial RNA from degradation
  • The 5’ NAD cap found in some eukaryotes actually promotes decay rather than provide protection.
  • 5’ 7-methylguanosine cap of eukaryotes: added post-transcription
  • 5’ NAD cap in prokaryotes and eukaryotes: added in initiation step of transcription
Overview of segments of mRNA

Overview of segments of messenger RNA (mRNA): including the 5’ cap and 3’ poly-A tail

Image by Lecturio.

Transfer RNA (tRNA)


  • Transfer RNA is a single polynucleotide made up of an average of 75 nucleotides.
  • Has modified bases such as inosine, dihydrouridine, and pseudouridine
  • The distinctive fold creates a 2-dimensional shape resembling a cloverleaf.
  • The 3-dimensional or tertiary structure of tRNA is actually L shaped.
  • Parts of tRNA consist of:
    • Acceptor stem:
      • Contains the 3’ CCA (cytosine-cytosine-adenine) sequence: 
        • Amino acid attachment site 
        • Forms a covalent bond to a specific amino acid via aminoacyl-tRNA synthetase
      • The acceptor stem also contains parts of the 5’ end of tRNA.
    • Anti-codon loop:
      • The 3-base sequence is complementary to the mRNA triplet code for the specific amino acid.
    • D-arm (contains dihydrouridine) and T-arm (pseudouridine loop) or TΨC arm (thymidine-pseudouridine-cytidine):
      • The D-arm is believed to be a recognition site for aminoacyl-tRNA synthetase.
      • The T-arm aids in ribosome attachment.
    • Variable loop:
      • May or may not be present; allows for further classification of tRNA
Transfer RNAs (tRNA)

Secondary structure of transfer RNA (tRNA): Notice that its entire sequence can be seen, indicating the reduced size.

Image by Lecturio.


Transfer RNA transports amino acids to ribosomes for assembly into proteins. This process is carried out by these 2 main actions:

  • Chemically links to a specific amino acid:
    • Specificity is due to the enzyme aminoacyl-tRNA synthetase
      • Each enzyme recognizes only one amino acid and the corresponding tRNA.
      • 20 aminoacyl-tRNA synthetase enzymes correspond to each of the 20 amino acids.
      • Uncharged tRNA: no amino acid attached
      • Charged tRNA: amino acid attached
    • Aminoacyl-tRNA synthetase links the amino acid to the 3’ terminal of the tRNA acceptor stem
  • Forms base pairs with the codon in the mRNA:
    • Via tRNA anti-codon loop
    • Determines the amino acid to carry to the ribosome for protein assembly
    • One tRNA carries one specific amino acid but one tRNA can read more than one codon.
    • More than one codon can code for one amino acid (codon degeneracy):
      • Example: 1 tRNA = 1 amino acid (Phe) = different codons, but the same first 2 bases: UUU, UUC
    • The first 2 codon bases: main determining bases for amino acids
    • Between the 3rd codon base and the complementary 1st anti-codon base of the tRNA, more than one base pair is possible: 
      • Can follow atypical base-pairing (wobbling)
      • Example: Inosine (I), a modified base found in tRNA, pairs with the uracil (U), adenine (A), and cytosine (C).
Translation and the role of tRNA

Translation and the role of tRNA

Image by Lecturio.
Aminoacids table

The degeneracy of the genetic code as shown by this codon wheel. Note that many amino acids are encoded by more than one combination of bases.

Image: “Aminoacids table” by Mouagip. License: Public Domain

Ribosomal RNA (rRNA)


Ribosomes consist of 2 subunits of unequally sized rRNA, and the sizes are measured in terms of an “S” value (Svedberg or sedimentation unit):

  • Based on a measure of sedimentation velocity in a centrifuge (higher “S” value = faster sedimentation = greater mass)
  • Therefore, “S” values are not additive.
  • Prokaryotic ribosomes: 70S consisting of 50S (large subunit) and 30S (small subunit)
  • Eukaryotic ribosomes: 80S consisting of 60S (large subunit)  and 40S (small subunit)
  • Has 3 functionally distinct tRNA binding sites:
    • Amino acyl (A) site (accepts incoming aminoacyl tRNA)
    • Peptidyl (P) site (for the peptidyl tRNA to which the growing peptide chain is attached)
    • Exit (E) site (where the deacylated tRNA exits the ribosome)
Table: Components of the 70S prokaryotic ribosome
50S5STransmit and coordinate functional centers of ribosome
23SPeptidyl transferase: peptide bond formation
30S16SBind initiation codon; ribosomal scaffold
Table: Components of the 80S eukaryotic ribosome
60S5SStructural support
28SPeptidyl transferase: peptide bond formation
Ribosome subunits large

Ribosome: large subunits

Image by Lecturio.
Ribosome subunits small

Ribosome: smallsubunits

Image by Lecturio.


  • Most abundant form of RNA in living cells (about 80% of total RNA in a cell)
  • Serves as a scaffold of the ribosomal subunits
  • Ribosomal RNA associates with proteins to form ribosomes (the site of protein synthesis).
  • Catalyzes specific chemical reactions (ribozymes: “ribo-” that acts like en-“zymes”)
  • Largest rRNA 23S (prokaryotes) and 28S (eukaryotes) in the large subunit of the ribosome:
    • The most important ribozyme
    • Ribosomal RNA is a peptidyl transferase (it catalyzes peptide bond formation between amino acids to form proteins).
  • Note the differences:
    • Ribosomal RNA: rRNA
    • Ribosome: rRNA + proteins
    • Ribozyme: rRNA with enzyme-like activity, catalyzing protein synthesis in ribosomes

Other Forms of RNA

RNA processing

Small nuclear RNA:

  • Non-coding RNA (eukaryotes) 
  • Associates with proteins to form small nuclear ribonucleoproteins (snRNPs):
    • Small nuclear ribonucleoproteins (snRNPs) + protein = spliceosome
    • Spliceosomes excise introns from a transcribed pre-mRNA (splicing).
    • Key for rRNA and mRNA processing and gene regulation

Small nucleolar RNA:

  • Non-coding RNA (eukaryotes)
  • Modifies RNA nucleotides

Gene regulation

Micro RNA:

  • Non-coding RNA (eukaryotes)
  • Regulates degradation and translation of mRNA
  • Abnormal expression of miRNA can contribute to malignancy development (functioning as oncogenes or tumor suppressors).

Small regulatory RNA:

  • Non-coding RNA (prokaryotes)
  • Gene regulation


  • Transcription regulation

Genome defense

Small interfering RNA:

  • Non-coding RNA (eukaryotes)
  • Silencing RNA
  • Operates within the RNA interference (RNAi) pathway (with miRNA)
  • Defense against foreign RNA

PIWI-interacting RNA:

  • Non-coding RNA (eukaryotes)
  • Regulates gene expression and fights viral infection


  • Non-coding RNA (prokaryotes)
  • Defense against foreign DNA and RNA

Other ribozymes

Ribonuclease P (RNAse P):

  • Cleaves pre-tRNA to generate the 5’ free end of mature tRNA

Self-splicing introns:

  • Introns in the genes act as ribozymes with nuclease activity.


  • Non-coding RNA
  • Naked RNA in plants
  • Cleaves itself during the viroid replicative cycle


  1. Weil, P. A. (2018). Nucleic acid structure & function. V. W. Rodwell, D. A. Bender, K. M. Botham, P. J. Kennelly & P. A. Weil (Eds.), Harper’s illustrated biochemistry, 31e. New York, NY: McGraw-Hill Education. accessmedicine.mhmedical.com/content.aspx?aid=1160190679
  2. McKee, T., & McKee, J. R. (2009). Biochemistry: The molecular basis of life. New York: Oxford University Press.
  3. Clark, D. P., Pazdernik, N., & McGehee, M. (2019). Molecular biology.

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