2.26 Ribonucleic Acid (RNA)

Introduction

Ribonucleic acid (RNA) is one of the two types of nucleic acids found in living organisms. Unlike DNA, RNA is generally single-stranded and does not form a double helix. RNA plays a central role in protein synthesis and carries out various other functions in the cell. It is a polymer of nucleotides, just like DNA, but differs in its sugar, bases, and structure.

Definition

Ribonucleic Acid (RNA): RNA is a polymer of nucleotides. It is generally single-stranded and does not form a double helix like DNA. However, some regions of RNA show a secondary double-stranded structure in their complementary regions.

In simple words: RNA is a nucleic acid that is usually single-stranded and helps in protein synthesis.

Core Concept

• RNA is a polymer of nucleotides.
• Its detailed chemical nature has already been discussed in previous topics (sugar, phosphate, nitrogenous bases).
• Unlike DNA, RNA is generally single-stranded.
• It does not form a double helix like DNA.
• However, some regions of RNA show a secondary double-stranded structure in their complementary regions.
• There are three major classes of RNA, each with a special function in protein synthesis.
• These RNAs are transcribed from DNA template.

Detailed Explanation

Chemical Nature of RNA

Composition:

• The sugar in RNA is ribose, which has an -OH group at the 2' position.
• The bases in RNA are A, U, G, C.
• Uracil (U) replaces Thymine (T) found in DNA.
• RNA is a linear, unbranched polymer of nucleotides.
• RNA is usually single-stranded.
• RNA can have secondary structure in some regions due to complementary base pairing within the same molecule.

Comparison of DNA and RNA

Types of RNA

There are three major classes of RNA, each with a special function in protein synthesis:

• Messenger RNA (mRNA)
• Ribosomal RNA (rRNA)
• Transfer RNA (tRNA)

These RNAs are transcribed from DNA template.

Why RNA is Single-Stranded

• RNA is usually single-stranded because it does not need to store genetic information for a long time.
• Its role is to carry out protein synthesis, which requires it to be flexible.
• The single-stranded nature allows RNA to fold into complex 3D shapes.
• These shapes are important for its functions (e.g., tRNA, rRNA).

Secondary Structure of RNA

• Although RNA is single-stranded, some regions can form double-stranded structures.
• This happens when complementary bases within the same RNA molecule pair with each other.
• Examples:
• tRNA – Cloverleaf structure with double-stranded regions.
• rRNA – Complex secondary structure.
• These secondary structures are important for the function of RNA.

Transcription of RNA from DNA

Definition: Transcription is the process by which RNA is synthesized from a DNA template.

• RNA is transcribed from DNA.
• The enzyme RNA polymerase catalyzes the reaction.
• The RNA sequence is complementary to the DNA template strand.
• In RNA, uracil (U) pairs with adenine (A) on the DNA template.
• RNA is synthesized in the 5' → 3' direction.

• DNA strands unwind.
• RNA polymerase binds to the promoter region.
• RNA polymerase adds complementary nucleotides.
• RNA chain elongates.
• RNA is released.
• DNA strands rewind.

Importance of RNA

Intermediate Level

RNA in Detail

Chemical Composition:

• Linear, unbranched polymer.
• Usually single-stranded.
• Can form secondary structures in some regions.

Comparison of DNA and RNA

Types of RNA

Transcription

Definition: Transcription is the process by which RNA is synthesized from a DNA template.

• Initiation: RNA polymerase binds to the promoter.
• Elongation: RNA polymerase adds complementary nucleotides.
• Termination: RNA polymerase reaches the terminator; RNA is released.

• DNA A → RNA U
• DNA T → RNA A
• DNA G → RNA C
• DNA C → RNA G

Why RNA is Less Stable Than DNA

• RNA has an -OH group at the 2' position of ribose.
• This -OH group can participate in reactions that cleave the phosphodiester bond.
• Therefore, RNA is less stable and is degraded more quickly.
• DNA lacks this -OH group, making it more stable.

Importance of RNA

Important Points

• 1. RNA is also a polymer of nucleotides.
• 2. Its detailed chemical nature has already been discussed in previous topics.
• 3. Unlike DNA, the RNA is generally single-stranded and does not form a double helix like DNA.
• 4. However, some regions of RNA show a secondary double-stranded structure in their complementary regions.
• 5. There are three major classes of RNA each with a special function in protein synthesis.
• 6. These RNA are transcribed from DNA template.
• 7. Types of RNA:
• - Messenger RNA (mRNA)
• - Ribosomal RNA (rRNA)
• - Transfer RNA (tRNA)
• 8. mRNA consists of a single strand of variable length.
• - Its length depends upon the size of the gene and the protein.
• - For a protein of 100 amino acids, mRNA has 300 nucleotides.
• - Every three nucleotides in mRNA encode a specific amino acid.
• - These triplets are called codons.
• - mRNA is about 3–4% of total RNA.
• - mRNA takes the genetic message from the nucleus to the ribosome.
• - This process is called translation.
• 9. rRNA is transcribed by genes on DNA.
• - It becomes part of ribosome.
• - Base sequence is similar from bacteria to higher plants and animals.
• - Largest size among RNA.
• - Approximately 80% of total RNA is rRNA.
• - Provides a platform for protein synthesis.
• 10. tRNA is the smallest RNA.
• - Consists of 75 to 90 nucleotides.
• - Single-stranded but shows duplex appearance at some regions.
• - Shows a cloverleaf shape in two-dimensional views.
• - 5' end terminates in guanine.
• - 3' end terminates with CCA.
• - Amino acid is attached at the 3' end.
• - Has three loops: D loop, anticodon loop, T loop.
• - The anticodon is complementary to a specific codon of mRNA.
• - At least one tRNA for each of the 20 amino acids.
• - Sixty tRNA have been identified.
• - Human cells contain about 45 different kinds of tRNA.

Remember

• - **RNA** = ribonucleic acid
• - **Sugar** = ribose
• - **Bases** = A, U, G, C
• - Structure = usually single-stranded
• - Function = protein synthesis
• - Transcribed from DNA
• - Three types: mRNA, rRNA, tRNA
• - mRNA = carries message; 3–4% of total RNA; codons
• - rRNA = makes ribosomes; 80% of total RNA; platform for protein synthesis
• - tRNA = brings amino acids; 75–90 nucleotides; cloverleaf; anticodon
• - tRNA ends: 5' guanine; 3' CCA
• - tRNA loops: D loop, anticodon loop, T loop
• - **Ribozymes** = catalytic RNA

Common Mistakes

• 1. Confusing RNA and DNA – RNA has ribose and uracil; DNA has deoxyribose and thymine.
• 2. Thinking RNA is always single-stranded – RNA is usually single-stranded but can have secondary double-stranded regions.
• 3. Thinking RNA is only in the cytoplasm – RNA is found in both the nucleus and the cytoplasm.
• 4. Confusing the three types of RNA – mRNA carries the message; rRNA makes ribosomes; tRNA brings amino acids.
• 5. Forgetting that uracil replaces thymine in RNA – RNA has U, not T.
• 6. Thinking mRNA is the most abundant RNA – rRNA is the most abundant (~80%); mRNA is the least abundant (3–4%).
• 7. Confusing codons and anticodons – Codons are on mRNA; anticodons are on tRNA.
• 8. Thinking tRNA has only one loop – tRNA has three loops: D loop, anticodon loop, T loop.
• 9. Forgetting the 5' and 3' ends of tRNA – 5' end is guanine; 3' end is CCA.
• 10. Thinking RNA is as stable as DNA – RNA is less stable than DNA because of the -OH group at the 2' position.
• 11. Confusing ribozymes with enzymes – Ribozymes are RNA molecules with catalytic activity; enzymes are usually proteins.
• 12. Thinking RNA only functions in protein synthesis – RNA also has catalytic, regulatory, and signaling functions.
• 13. Forgetting that some viruses use RNA as genetic material – HIV, influenza, and SARS-CoV-2 are RNA viruses.
• 14. Confusing the number of tRNA molecules – Sixty tRNA have been identified; human cells contain about 45 different kinds.

Quick Revision

• RNA is also a polymer of nucleotides.
• Its detailed chemical nature has already been discussed in previous topics.
• Unlike DNA, the RNA is generally single stranded and does not form a double helix like DNA.
• However, some regions of RNA shows a secondary double stranded structure in their complementary regions.
• There are three major classes of RNA each with a special function in protein synthesis.
• These RNA are transcribed from DNA template.
• mRNA consists of a single strand of variable length.
• Its length depends upon the size of the gene, as well as the protein for which it is taking message.
• For example, for a protein molecule consisting of 100 amino acids, the mRNA will have the length of 300 nucleotides.
• Actually every three nucleotides in mRNA encode a specific amino acid, such triplets of nucleotides along the length of mRNA are called codons of genetic codes.
• mRNA is about 3 to 4% of the total RNA in the cell.
• mRNA takes the genetic message from the nucleus to the ribosome in the cytoplasm to form particular protein.
• This process is known as translation.
• rRNA is transcribed by the genes present on the DNA of the several chromosomes.
• It is called rRNA because it eventually becomes part of ribosome.
• The rRNA is packaged with a variety of proteins into ribosomal subunits.
• The base sequence of rRNA is similar from bacteria to higher plants and animals.
• rRNA have largest size among the RNA.
• Approximately, 80% of total RNA contents of a cell are rRNA.
• It is a part of ribosome where protein synthesis takes place.
• In other words rRNA provides a platform for protein synthesis.
• tRNA is the smallest of the RNA molecules and it consists of 75 to 90 nucleotides.
• A tRNA is a single stranded molecule but it shows a duplex appearance at its some regions where complement entry bases are bonded to one another.
• It shows a flat cloverleaf shape in two dimensional views.
• Its 5' end always terminates in Guanine base while the 3' end is always terminated with base sequence of CCA.
• Amino acid is attached to tRNA at this end.
• The nucleotide sequence of the rest of the molecule is variable.
• tRNA has three loops.
• The middle loop in all the tRNA is composed of 7 bases, the middle three of which form the anticodon; it is complementary to specific codon of mRNA.
• The D loop recognizes the activation enzyme.
• Theta (θ) loop recognizes the specific place on the ribosome for binding during protein synthesis.
• There is at least one tRNA molecule for each of the 20 amino acids found in proteins.
• Sixty tRNA have been identified.
• However, human cells contain about 45 different kinds of tRNA molecules, each transports a specific amino acid from cytoplasm to the surface of ribosome for protein synthesis.
• Science, Technology and Society Connections: Correlate the scanning tunnelling microscope as the latest advancement for seeing the atoms of DNA.
• The Scanning tunneling microscope was invented in 1980.
• It can allow scientists to view atoms on the surface of a solid.
• It is a very powerful tool that can be used to resolve features less than a nanometer.
• The microscope's inventors, Gerd Binnig and Heinrich Rohrer were awarded Nobel Prize in Physics in 1986.
• Seeman's group worked on the DNA nanotechnology. They constructed molecular building blocks of DNA.

60-Second Revision

• **RNA** = ribonucleic acid
• **Sugar** = ribose
• **Bases** = A, U, G, C
• Structure = usually single-stranded
• Function = protein synthesis
• Transcribed from DNA
• Three types: mRNA, rRNA, tRNA
• mRNA = carries message; 3–4% of total RNA; codons
• rRNA = makes ribosomes; 80% of total RNA; platform for protein synthesis
• tRNA = brings amino acids; 75–90 nucleotides; cloverleaf; anticodon
• tRNA ends: 5' guanine; 3' CCA
• tRNA loops: D loop, anticodon loop, T loop
• **Ribozymes** = catalytic RNA
• Warning: RNA has ribose and uracil; DNA has deoxyribose and thymine. RNA is usually single-stranded but can have secondary structures. rRNA is the most abundant; mRNA is the least abundant. Codons are on mRNA; anticodons are on tRNA. tRNA has three loops. RNA is less stable than DNA. Some viruses use RNA as genetic material.