DNA & RNA Structure (DP IB Biology: SL)

• The nucleic acids DNA and RNA are polymers of 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 (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 basic structure of a nucleotide

• 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

• 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

• This sequence is the basis of the genetic code as a store of genetic information

• 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)

An RNA nucleotide compared with a DNA nucleotide

• Unlike DNA, RNA molecules are only made up of one polynucleotide strand (they are single-stranded)
• Unlike DNA, RNA polynucleotide chains are relatively short compared to DNA
• Like DNA, the sugar-phosphate bonds (between different nucleotides in the same strand) are strong covalent bonds
• Like DNA, the nitrogenous bases stick out sideways from the sugar-phosphate backbone

The structure of RNA

Nucleotide Structure Summary Table

• 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

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 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

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

• Francis Crick and James Watson were two Cambridge scientists who worked together to establish the double helix structure of DNA in 1953
• They used data from their previous experiments on the composition of DNA
• Published findings from other research labs played a role in developing their model
  • Rosalind Franklin, Edwin Chargaff and Linus Pauling, all of whom were leading research efforts in other universities, contributed important data to Crick & Watson's discovery
  • This suggests that there was a close-knit collaboration, but in fact, there was a lot of competition between the groups to make the breakthrough discovery

• Physical model-making played a large role in their success
• Early versions of the model were rejected for various reasons
  • It was not compact enough
  • It would have been too unstable (DNA is a highly stable molecule)
  • It did not allow equivalent amounts of A and T, and C and G bases to be present (Chargaff's findings)
  • It fitted together much better once the second strand was flipped to become antiparallel

• Their final model was constructed carefully with clamps, metal rods for bonds and with the correct bond angles
• Their model was the basis of a lot of genetic research globally in the years that followed
  • Notably, Crick and Watson's model sparked work to prove the way in which DNA replicates in cells

NOS: Using models as a representation of the real world; Crick and Watson used model making to discover the structure of DNA

• Models in science are built to represent concepts and ideas in a way that can be pictured by our brains
• Models can be accepted or rejected based on experimental data generated by further research
• Crick and Watson built physical, scale models of DNA to explain biological observations
  • Using simple laboratory equipment (clamps, stands, metal rods etc)
  • They adapted their models by making them more realistic eg. by building in the correct bond angles within molecules

• They built successive models, using trial-and-error to arrive at the finalised model
• Their first model of DNA was rejected, based on the findings of Rosalind Franklin
  • Crick and Watson received the Nobel prize for their work
  • Franklin died aged 37 so never received the recognition she deserved for her significant role in defining DNA structure

• Today, sophisticated computer modelling is performed, that
  • Takes the place of physical model-making and provides further explanation of the functions of various biomolecules
  • Shortens the 'trial-and-error' cycles of model-making as experienced by Crick and Watson