Nucleotides, DNA & RNA, Base Pairing (Edexcel International AS Biology): Revision Note

Nucleotides

• 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

Polynucleotides: DNA & RNA

• 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

Base Pairing in the DNA Double Helix

• 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