DNA & RNA Structure (SL IB Biology)

DNA as the genetic material of living organisms

• Deoxyribose nucleic acid (DNA) carries the genetic code in all living organisms
• This is the reason why the genetic code is said to be universal, it applies to all forms of life
• DNA is mainly found in the nucleus where it forms chromosomes
  • It is also found in chloroplasts and mitochondria of eukaryotic cells
• Ribonucleic acid (RNA) is another type of nucleic acid which is the main component of ribosomes, which play an important role in protein synthesis 
  • Some RNA is also found in the nucleus and cytoplasm
• Certain viruses (such as SARS-CoV-2) contain RNA as their genetic material instead of DNA
• These viruses cause a variety of different diseases, such as COVID-19, Ebola, mumps and influenza
• Viruses are not considered to be living organisms, since they are unable to replicate by themselves
• They are dependent on other living cells for replication and survival
• Viruses also lack a cellular structure, which is another reason they are not considered to be living

Components of a nucleotide

• 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 (with either 1 or 2 rings of atoms)
  • A phosphate group (this is acidic and negatively charged)
• The base and phosphate group are both covalently bonded to the sugar
• The nitrogenous bases in DNA are:
  • Adenine (A)
  • Guanine (G)
  • Cytosine (C)
  • Thymine (T)
• RNA share the same nitrogenous bases as DNA except thymine, which is replaced by uracil (U) in RNA
• The nitrogenous bases can be grouped as either purine or pyrimidine bases:
  • Adenine and guanine are purine bases
  • Cytosine, thymine (in DNA) and uracil (in RNA) are pyrimidine bases

Nucleotide structure diagram

The basic structure of a nucleotide

Drawing simple diagrams of the structure of single nucleotides of DNA and RNA

• Simple shapes can be used to draw the main building blocks of nucleotides and the DNA double helix
  • Advanced drawing skills are not required!
• Pentagons can represent pentose sugars
• Circles can represent phosphates
  • Often shown as a circle with the letter P inside: ℗
• Rectangles can represent bases
• Covalent bonds can be shown with solid lines
• Hydrogen bonds can be shown with dashed lines
  • Or with complementary shapes that fit together (see diagrams)

Components of a nucleotide diagram

Simple shapes can be used to represent parts of nucleotide molecules

Forming the sugar-phosphate backbone

• Nucleotides join together in chains to form DNA or RNA strands
• The phosphate group of one nucleotide forms a covalent bond to the pentose sugar of the next one 
  • This carries on to form a large polymer
  • These polymers form nucleic acids, which are also known as polynucleotides
• The phosphate group of one nucleotide is linked to the pentose sugar of the next one by condensation reactions
  • This means a molecule of water is released during the formation of each covalent bond
• This forms a 'sugar-phosphate backbone' with a base linked to each sugar
• The polymer of nucleotides is known as a strand
• DNA is double-stranded, RNA is usually single-stranded
• There are just 4 separate bases that can be joined in any combination/sequence
  • Because the sugar and phosphate are the same in every nucleotide

Linking nucleotides together diagram

Two nucleotides shown bonded together covalently within a strand

RNA structure

• Unlike DNA, RNA molecules are relatively short with lengths of between a hundred to a few thousand nucleotides
• It usually forms a single-stranded polynucleotide with ribose as the pentose sugar in each nucleotide
• RNA nucleotides contain the following nitrogenous bases:
  • Adenine
  • Guanine
  • Cytosine
  • Uracil (instead of thymine in DNA)
• The carbon atoms in nucleotides are numbered from the right in a clockwise direction
  • This makes it easier to identify the bonds in the sugar-phosphate backbone of polynucleotides
  • It also indicates the orientation of the polynucleotide

RNA nucleotide diagram

The structure of an RNA nucleotide

• Different types of RNA are found in the cells of living organisms:
  • messenger RNA (mRNA), which is formed in the nucleus and transported to the ribosomes in the cytoplasm
  • transfer RNA (tRNA), which is responsible for transporting amino acids to ribosomes during protein synthesis
  • ribosomal RNA (rRNA), which forms part of ribosomes
• Adjacent RNA nucleotides are linked together by condensation reactions, during which a molecule of water is released
• This forms a phosphodiester bond between the pentose sugar of one nucleotide and the phosphate group of the next nucleotide

The formation of an RNA polymer diagram

Linking RNA nucleotides together by condensation reactions will result in the formation of phosphodiester bonds

DNA structure

• DNA is a double helix made of two antiparallel strands of nucleotides linked by hydrogen bonding between complementary base pairs
• The nucleic acid DNA is a polynucleotide – it is made up of many nucleotides bonded together in a long chain

DNA nucleotide diagram

A DNA nucleotide

• 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
• Each DNA polynucleotide strand is said to have a 3’ end and a 5’ end (these numbers relate to which carbon atom on the pentose sugar could be bonded with another nucleotide)
• Because 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 diagram

A single DNA polynucleotide strand showing 3 nucleotides in a sequence

Hydrogen bonding

• 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

DNA molecule with hydrogen bonding diagram

A section of DNA – two antiparallel DNA polynucleotide strands held together by hydrogen bonds

Double helix

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

DNA double helix formation diagram

DNA molecules form a three-dimensional structure known as a DNA double helix

Drawing base-pairing in a DNA molecule

When drawing the base pairing, the opposite strand should be antiparallel to the first. The presence of hydrogen bonding is shown, but the numbers/lengths of bonds is not required