2.9 Nucleotides, DNA & RNA, Base Pairing

• Both DNA and RNA are polymers that are made up of many repeating units called nucleotides
• Each nucleotide is formed from:
  • A pentose sugar (a sugar with 5 carbon atoms)
  • A nitrogen-containing organic base
  • A phosphate group

The basic structure of a mononucleotide

DNA nucleotides

• The components of a DNA nucleotide are:
  • A deoxyribose sugar with hydrogen at the 2' position
  • A phosphate group
  • One of four nitrogenous bases - adenine (A), cytosine(C), guanine(G) or thymine(T)

RNA nucleotides

• The components of an RNA nucleotide are:
  • A ribose sugar with a hydroxyl (OH) group at the 2' position
  • A phosphate group
  • One of four nitrogenous bases - adenine (A), cytosine(C), guanine(G) or uracil (U)
• The presence of the 2' hydroxyl group makes RNA more susceptible to hydrolysis
  • This is why DNA is the storage molecule and RNA is the transport molecule with a shorter molecular lifespan

RNA nucleotide compared with a DNA nucleotide

Purines & Pyrimidines

• The nitrogenous base molecules that are found in the nucleotides of DNA (A, T, C, G) and RNA (A, U, C, G) occur in two structural forms: purines and pyrimidines
  • The bases adenine and guanine are purines – they have a double ring structure
  • The bases cytosine, thymine and uracil are pyrimidines – they have a single ring structure

The molecular structure of each base is different, depending on whether they are a purine or pyrimidine

• DNA and RNA are polymers (polynucleotides), meaning that they are made up of many nucleotides joined together in long chains
• Separate nucleotides are joined via condensation reactions
  • These condensation reactions occur between the phosphate group of one nucleotide and the pentose sugar of the next nucleotide
• A condensation reaction between two nucleotides forms a phosphodiester bond
  • It is called a phosphodiester bond because it consists of a phosphate group and two ester bonds (phosphate with double bond oxygen attached - oxygen - carbon)
• The chain of alternating phosphate groups and pentose sugars produced as a result of many phosphodiester bonds is known as the sugar-phosphate backbone (of the DNA or RNA molecule)

A section of a polynucleotide showing a single phosphodiester bond (and the positioning of the two ester bonds and the phosphate group that make up the phosphodiester bond)

DNA structure

• The nucleic acid DNA is a polynucleotide – it is made up of many nucleotides bonded together in a long chain
• DNA molecules are made up of two polynucleotide strands lying side by side, running in opposite directions – the strands are said to be antiparallel
• Each DNA polynucleotide strand is made up of alternating deoxyribose sugars and phosphate groups bonded together to form the sugar-phosphate backbone. These bonds are covalent bonds known as phosphodiester bonds
  • The phosphodiester bonds link the 5-carbon of one deoxyribose sugar molecule to the phosphate group from the same nucleotide, which is itself linked by another phosphodiester bond to the 3-carbon of the deoxyribose sugar molecule of the next nucleotide in the strand
  • Each DNA polynucleotide strand is said to have a 3’ end and a 5’ end (these numbers relate to which carbon on the pentose sugar could be bonded with another nucleotide)
  • As the strands run in opposite directions (they are antiparallel), one is known as the 5’ to 3’ strand and the other is known as the 3’ to 5’ strand
• The nitrogenous bases of each nucleotide project out from the backbone towards the interior of the double-stranded DNA molecule

A single DNA polynucleotide strand

RNA structure

• Like DNA, the nucleic acid RNA (ribonucleic acid) is a polynucleotide – it is made up of many nucleotides linked together in a chain
• Like DNA, RNA nucleotides contain the nitrogenous bases adenine (A), guanine (G) and cytosine (C)
• Unlike DNA, RNA nucleotides never contain the nitrogenous base thymine (T) – in place of this they contain the nitrogenous base uracil (U)
• Unlike DNA, RNA nucleotides contain the pentose sugar ribose (instead of deoxyribose)
• Unlike DNA, RNA molecules are only made up of one polynucleotide strand (they are single-stranded)
• RNA polynucleotide chains are relatively short compared to DNA
• Each RNA polynucleotide strand is made up of alternating ribose sugars and phosphate groups linked together, with the nitrogenous bases of each nucleotide projecting out sideways from the single-stranded RNA molecule
• The sugar-phosphate bonds (between different nucleotides in the same strand) are covalent bonds known as phosphodiester bonds
  • These bonds form what is known as the sugar-phosphate backbone of the RNA polynucleotide strand
  • The phosphodiester bonds link the 5-carbon of one ribose sugar molecule to the phosphate group from the same nucleotide, which is itself linked by another phosphodiester bond to the 3-carbon of the ribose sugar molecule of the next nucleotide in the strand
• An example of an RNA molecule is messenger RNA (mRNA), which is the transcript copy of a gene that encodes a specific polypeptide. Two other examples are transfer RNA (tRNA) and ribosomal RNA (rRNA)

Messenger RNA (mRNA) is an example of the structure of RNA

• The two antiparallel DNA polynucleotide strands that make up the DNA molecule are held together by hydrogen bonds between the nitrogenous bases
• These hydrogen bonds always occur between the same pairs of bases:
  • The purine adenine (A) always pairs with the pyrimidine thymine (T) – two hydrogen bonds are formed between these bases
  • The purine guanine (G) always pairs with the pyrimidine cytosine (C) – three hydrogen bonds are formed between these bases
  • This is known as complementary base pairing
  • These pairs are known as DNA base pairs

A section of DNA showing hydrogen bonding between base pairs

Double helix

• DNA is not two-dimensional as seen in the diagram above
• DNA is described as a double helix
• This refers to the three-dimensional shape that DNA molecules form

DNA molecules form a 3D double helix structure