Nucleic Acids: Nucleotides, Sugars and Nitrogenous Bases

• Nucleic acids are long chains (polymers) of repeating subunits called nucleotides
• Each nucleotide subunit is composed of a five-carbon sugar, a phosphate group, and a base

Five-Carbon Sugars

• Nucleotide subunits of RNA contain ribose, a pentose sugar
• Nucleotide subunits of DNA contain deoxyribose
• The carbon atoms in pentose sugars are numbered 1' through 5'
• Primes differentiate sugar ring positions from base positions
• Both sugars have an oxygen in the five-member ring, with the 5' carbon outside the ring
• Sugars differ by the presence/absence of oxygen at the 2' position which significantly impacts function

Nitrogenous Bases

• Bases are nitrogen-containing molecules with chemical properties of a base
• Adenine (A) and guanine (G) are purines, having a double carbon-nitrogen ring structure
• Thymine (T), cytosine (C), and uracil (U) are pyrimidines, with a single ring structure
• Thymine is found only in DNA
• Uracil is specific to RNA

Nucleosides and Nucleotides

• DNA or RNA chains form in three steps
• 1. A base chemically links to a sugar molecule at the 1' carbon, forming a nucleoside
• 2. A phosphate group attaches to the 5' carbon of the sugar, and the nucleoside becomes a nucleotide
• 3. Nucleotides join (polymerize) via condensation reactions to form a chain
• The hydroxyl group on the 3' carbon of one sugar nucleotide forms an ester bond to the phosphate of another nucleotide, eliminating water
• This chemical bond is a phosphodiester bond, or 5' → 3' phosphodiester bond, and indicates strand polarity

Significance of 5' and 3'

• The ends of DNA or RNA chains have distinct chemical properties designated as 5' and 3'
• 5' indicates the carbon in the sugar where the phosphate (PO4) functional group is attached
• 3' refers to the carbon in the sugar ring where a hydroxyl (OH) functional group is attached
• Understanding directionality (polarity) is critical for aspects of replication, transcription, reading DNA sequences, and lab experiments
• By convention, a DNA sequence is written with the 5' end to the left, and the 3' end to the right

Nomenclature of Nucleotides

• Nucleotides contain one phosphate unit (monophosphate), two (diphosphate), or three (triphosphate)
• When incorporated, a nucleotide contains one of each component
• Free nucleotides usually occur as triphosphates forming a precursor building block for DNA or RNA chain synthesis

The Length of RNA and DNA

• Cellular RNAs range from less than one hundred to thousands of nucleotides (nt) or bases
• Cellular DNA molecules can be several hundred million nucleotides long
• The number of base pairs (bp) measures the length of double-stranded DNA
• A kilobase pair (kb or kbp) refers to 1000 base pairs
• Researchers often use short chains of single-stranded DNA (less than 50 bases) called oligonucleotides

Double-Stranded DNA Forms a Double Helix

• Two helical polynucleotide chains coil around a common axis
• The backbone is sugar-phosphate with bases projecting inside
• Polynucleotide chains run in opposite directions: one chain has 5' P → 3' OH polarity, the other has 3' OH → 5' P
• Two chains are held together by hydrogen bonds between bases
• Three hydrogen bonds occur between cytosine and guanine (C≡G)
• Two hydrogen bonds occur between adenine and thymine (A=T)
• The helix diameter is 20 Å and bases are separated by 3.4 Å along the helix axis and are related by a 36° rotation
• The helical structure repeats after 10 residues per chain at 34 Å intervals
• The DNA double helix is double-stranded DNA (dsDNA) or duplex DNA, to distinguish from single-stranded DNA (ssDNA)

Major and Minor Grooves

• Minor and major grooves form on opposite sides of the base pairs
• Minor grooves form where sugar-phosphate backbones are far apart
• Major grooves form where sugar-phosphate backbones are close together

DNA Types

• There are three different DNA types: A-DNA, B-DNA, and Z-DNA
• A-DNA is a right-handed double helix similar to B-DNA and forms when dehydrated to protect during extreme conditions
• B-DNA is the most common conformation of DNA under normal physiological conditions and is a right-handed helix
• Z-DNA is a left-handed DNA in a zig-zag pattern and may play a role in gene regulation

RNA Structure

• RNA is typically a single-stranded biopolymer that forms complex structures with bulges and helices
• This structure is critical for stability and function
• The ribose sugar and nitrogenous bases can be modified by cellular enzymes
• These modifications enable the formation of chemical bonds, leading to complex contortions stabilizing the RNA structure

Types and Functions of RNA

• Messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA) are the three types present in all organisms
• Messenger RNA is a long, unfolded RNA which constitutes 3-5% of the total RNA content
• It carries instruction from DNA, bringing the information of particular polypeptide types to be synthesized
• A base sequence is complementary to DNA at protein synthesis sites (ribosomes), and they participate in codon-anticodon interaction with tRNA
• Informational, messenger, or template RNAs (mRNAs) synthesize inside the nucleus and serve to transport genetic information to the cytoplasm for protein production
• From the two strands of DNA, only a template or noncoding or anti-sense strand transcribes mRNA
• 5' end has a methylated structure, does not translate
• Has 10-100 nucleotides, rich in U and A bases, does not translate
• AUG, codes for methionine amino acid
• About 1500 nucleotides on an average, translate proteins
• Either of UAA, UAG or UGA are present, and helps in translation termination
• Made of 50-150 nucleotides, does not translate, and has a sequence like AAUAAA
• 200-250 A nucleotides, does not translate, and makes the tail of mRNA

tRNA Structure

• tRNA or transfer RNA is an adapter molecule which helps in the synthesis of protein from mRNA
• It enables tRNA to link amino acids to nucleic acids and decipher the codon for the same in the mRNA molecule
• tRNAs are generally 76-90 nucleotides long
• Each amino acid has specific tRNAs
• Stop codons are not recognised by any tRNAs
• A secondary structure of tRNA looks like a clover leaf
• A tertiary structure is like an inverted 'L' shape
• This folded structure forms due to hydrogen bonding between complementary bases

Parts of Cloverleaf Structure

• Acceptor arm acts as the site of attachment for amino acids, this region is also called amino acid carrier arm
• Anti-codon loop contains a three-nucleotide sequence that is complementary to the codon of mRNA
• It consists of 7 unpaired bases, 3 of which make up the anti-codon, where tRNA attaches to mRNA to transport amino acids
• DHU loop is composed of three or four base pairs, variable in size with 8-12 unpaired bases
• It helps in binding of amino-acyl synthetase and has modified bases called dihydrouridine
• T oC loop is named because of triplet sequence of pseudouridine (φ) and acts as ribosome recognize arm
• It helps in determining the site of ribosome where the tRNA has to come and attach during translation
• The extra arm has variable nucleotide composition and is lacking in some tRNAs

rRNA Structure

• Ribosomal RNA forms about 80% of the total cellular RNA and consists of a single-stranded RNA
• RNA has regions that get twisted because of complementary base pairing
• R-RNA strand unfold on heating and refold on coiling
• It is one the most stable RNA among all types of RNAs, and rRNA and ribo-proteins constitute ribosomes