IB Biology SL

Revision Notes

2.5.1 DNA & RNA Structure

Nucleotide Structure & the Phosphodiester Bond

  • 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

Basic structure of a nucleotide, downloadable AS & A Level Biology revision notes

The basic structure of a nucleotide

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

Comparison between RNA nucleotide and DNA nucleotide, downloadable AS & A Level Biology revision notes

An RNA nucleotide (top) compared with a DNA nucleotide (bottom)

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

Purines and pyrimidines (1), downloadable AS & A Level Biology revision notesPurines and pyrimidines (2), downloadable AS & A Level Biology revision notes

The molecular structures of purines and pyrimidines are slightly different

Nucleotide Structure Table

Table 25 Nucleotide structure, downloadable AS & A Level Biology revision notes

Phosphodiester bonds

  • 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)

Phosphodiester bond in a polynucleotide strand, downloadable AS & A Level Biology revision notes

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

Exam Tip

Although DNA and RNA nucleotides are very similar, make sure you know the key differences between them: unlike DNA, RNA nucleotides never contain the nitrogenous base thymine (in place of this they contain the nitrogenous base uracil) and unlike DNA, RNA nucleotides contain the pentose sugar ribose (instead of deoxyribose).

You don’t need to know the structural formulae of the bases, just which are purines and which are pyrimidines.

The Structure of RNA

  • 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)

Comparison between RNA nucleotide and DNA nucleotide, downloadable AS & A Level Biology revision notes

An RNA nucleotide compared with a DNA nucleotide

  • 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)

mRNA as an example of RNA structure, downloadable AS & A Level Biology revision notes

Messenger RNA (mRNA) provides a good example of the structure of RNA

Exam Tip

You need to know the difference between DNA and RNA molecules (bases, number of strands, pentose sugar present, length).

The Structure of DNA

  • The nucleic acid DNA is a polynucleotide – it is made up of many nucleotides bonded together in a long chain

DNA polynucleotide strand, downloadable AS & A Level Biology revision notes, downloadable AS & A Level Biology revision notes

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. 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

DNA polynucleotide strand (2), downloadable AS & A Level Biology revision notes

A single DNA polynucleotide strand showing the positioning of the ester bonds

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, downloadable AS & A Level Biology revision notes

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

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 double helix formation, downloadable AS & A Level Biology revision notes

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

Exam Tip

Make sure you can name the different components of a DNA molecule (sugar-phosphate backbone, nucleotide, complementary base pairs, phosphodiester bonds, hydrogen bonds) and make sure you are able to locate these on a diagram.

Remember that phosphodiester bonds join the nucleotides in the sugar-phosphate backbone, and hydrogen bonds join the bases of the two complementary strands together

Remember that the bases are complementary, so the number of A = T and C = G. You could be asked to determine how many bases are present in a DNA molecule if given the number of just one of the bases.

Note that knowledge of purines and pyrimidines is not required

Evaluating the Watson-Crick Model

  • Watson and Crick were two scientists who worked together to confirm the double-helix structure of DNA in 1953
  • Watson and Crick also came up with a model by which DNA might be replicated:
    • This theory was called semi-conservative DNA replication
    • The theory is based upon the specific hydrogen bonding between pairs of nitrogenous bases (A+T and C+G) being used during replication to conserve the genetic sequence
  • However, this was just a theory, another theory suggested DNA replicated ‘conservatively’
    • The theory of conservative DNA replication suggested that the strands of the original DNA molecule would stay together, and the new, replicated DNA molecule would be made out of two brand new strands
  • Watson and Crick’s theory of semi-conservative DNA replication was later proved to be correct by the work of two other scientists, Meselson and Stahl
    • They used bacteria and two nitrogen isotopes, a heavy form (15N) and the normal, lighter form (14N), to prove this

Meselson and Stahl’s Experiment

  • Bacteria are grown in a broth containing the heavy (15N) nitrogen isotope
    • DNA contains nitrogen in its bases
    • As the bacteria replicated, they used nitrogen from the broth to make new DNA nucleotides
    • After some time, the culture of bacteria had DNA containing only heavy (15N) nitrogen
  • A sample of DNA from the 15N culture of bacteria was extracted and spun in a centrifuge
    • This showed that the DNA containing the heavy nitrogen settled near the bottom of the centrifuge tube
  • The bacteria containing only 15N DNA was then taken out of the 15N broth and added to a broth containing only the lighter 14N nitrogen. The bacteria were left for enough time for one round of DNA replication to occur before their DNA was extracted and spun in a centrifuge
    • If conservative DNA replication had occurred, the original template DNA molecules would only contain the heavier nitrogen and would settle at the bottom of the tube, whilst the new DNA molecules would only contain the lighter nitrogen and would settle at the top of the tube
    • If semi-conservative replication had occurred, all the DNA molecules would now contain both the heavy 15N and light 14N nitrogen and would therefore settle in the middle of the tube (one strand of each DNA molecule would be from the original DNA containing the heavier nitrogen and the other (new) strand would be made using only the lighter nitrogen)
  • Meselson and Stahl confirmed that the bacterial DNA had undergone semi-conservative replication.
    • The DNA from this second round of centrifugation settled in the middle of the tube, showing that each DNA molecule contained a mixture of the heavier and lighter nitrogen isotopes
    • If more rounds of replication were allowed to take place, the ratio of 15N:14would go from 1:1 after the first round of replication, to 3:1 after the second and 7:1 after the third
  • This experiment proved Watson and Crick’s theory correct

Meselson and Stahl Experiment (1), downloadable AS & A Level Biology revision notesMeselson and Stahl Experiment (2), downloadable AS & A Level Biology revision notes

Meselson and Stahl’s experiment that showed bacterial DNA replicated via semi-conservative DNA replication

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