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Chapter 8 Nucleic acids Background e-Learning Objectives Polynucleotides The structure of DNA It is amazing to realise that until the middle of the 20th century we did not even know that DNA is the genetic material. Our DNA carries the genetic code – a set of instructions telling the cell the sequence in which to link together amino acids when proteins are being synthesised. Slight differences in the structure of these proteins may result in slight differences in our metabolic reactions. Partly for this reason, we are all slightly different from one another. You probably know that DNA is a ‘double helix’. A DNA molecule is made of two long chains of nucleotide molecules, linked together to form a twisted ladder. Each chain is called a polynucleotide. DNA stands for deoxyribonucleic acid. When it was discovered, it was given the name ‘nucleic acid’ because it was mostly found in the nuclei of cells and is slightly acidic. Each nucleotide in a DNA molecule contains: a phosphate group the five-carbon sugar, deoxyribose an organic base. Figure 8.1 shows the components of a nucleotide in DNA. The base can be any one of four. These are adenine, guanine, thymine and cytosine. They are usually abbreviated to A, G, T and C. Adenine and guanine each contain two rings in their structure. They are known as purine bases. Thymine and cytosine have only one ring. They are known as pyrimidine bases. phosphate • • • deoxyribose organic bases purine bases adenine guanine pyrimidine bases adenine thymine thymine Figure 8.1 The components of a nucleotide in DNA. 124 cytosine Chapter 8: Nucleic acids Figure 8.2 shows how these components are linked in nucleotides and how the nucleotides link together to form long chains called polynucleotides. You can see that the base in each nucleotide sticks out sideways from the chain. In DNA, two chains of nucleotides lie side by side, one chain running one way and the other in the opposite direction (Figure 8.3 and Figure 8.4). They are said to be anti-parallel. The bases of one chain link up with the bases of the other by means of hydrogen bonds. The whole molecule twists to produce the double helix shape. nucleotide phosphate five-carbon sugar base condensation reaction polynucleotide The ‘direction’ of a polynucleotide 5´ end 5 1 4 3 2 3´ end The carbon atoms of the five-carbon sugar are numbered. The top phosphate is attached to carbon 5, so is at the 5´ end. The bottom phosphate is attached to carbon 3, so is at the 3´ end. Figure 8.2 How nucleotides join to form a polynucleotide. 125 Chapter 8: Nucleic acids The key to the ability of DNA to hold and pass on the code for making proteins in the cell is the way in which these bases link up. There is just the right amount of space for one large base – a purine – to link with one smaller base – a pyrimidine. And the linking is even more particular than that. A can only link with T, and C can only link with G. This is called complementary base pairing. Complementary base pairing ensures that the code carried on a molecule of DNA can be copied perfectly over and over again, so that it can be passed down from cell to cell and from generation to generation. It is also what enables the code on the DNA to be used to instruct the protein-making machinery in a cell to construct exactly the right proteins. You will find out much more about this if you continue studying biology to A2 level. antiparallel polynucleotide strands of DNA 3´ end 5´ end 5´ end 3´ end The two polynucleotide strands are twisted round forming a double helix. Figure 8.3 The structure of DNA. 5´ end The polynucleotide strands are held together by hydrogen bonding between the bases. 3´ end G C hydrogen bonds between a T–A complementary base pair T A 3´ end 5´ end Figure 8.4 Hydrogen bonding joining the bases in DNA. 126 Chapter 8: Nucleic acids DNA replication We have seen that, before a cell divides by mitosis, its DNA replicates to produce two copies. One copy is passed on to each daughter cell. DNA replication takes place during interphase of the cell cycle (Chapter 3). Figure 8.5 and Figure 8.6 show how DNA replication takes place. This method is called semiconservative replication, because each of the new DNA molecules is made of one old strand and one new strand of DNA. 1 Hydrogen bonds between the bases are broken. SAQ 1 One end of a DNA strand is called the 5´ (‘five prime’) end, and the other is the 3´ end. Why are they given these Answer names? Extension 2 Free nucleotides are present in the nucleus. 3 Free nucleotides pair up with complementary exposed bases. 4 The new strand is linked together. 3´ end 5 There are now two DNA molecules. Each one contains one old strand and one new one. Figure 8.5 DNA replication. DNA helicase unwinds and unzips the DNA by breaking the hydrogen bonds between bases. 3´ end 5´ end DNA polymerase links the newly arrived nucleotides by forming covalent bonds between phosphates and sugars. It only does this if the nucleotides are correctly paired. Figure 8.6 Enzymes are involved in DNA replication. 127 Chapter 8: Nucleic acids The role of DNA The structure of RNA DNA carries a code that is used by the cell when making proteins. The sequence of bases in the DNA molecules determines the sequence of amino acids that are strung together when a protein molecule is made on the ribosomes. A length of DNA that codes for making one polypeptide is called a gene. It is thought that there are around 30 000 genes in our cells (Figure 8.7). The code is read in groups of three ‘letters’ – that is, triplets of bases. As we have seen, there are four bases in a DNA molecule, A, T, C and G. A sequence of three bases in a DNA molecule codes for one amino acid (Figure 8.8). DNA is not the only polynucleotide in a cell. There are also polynucleotides which contain the sugar ribose rather than deoxyribose. They are therefore called ribonucleic acids, or RNA for short. Figure 8.9 shows the structure of RNA. RNA is generally single stranded, while DNA is generally double stranded. Another difference between them is that RNA always contains the base uracil (U) instead of thymine. While DNA stores the genetic information in the nucleus of a cell, RNA is involved with using that information to make proteins. U ribose uracil G C Figure 8.7 The Human Genome Project has worked out the base sequence in each human chromosome. These three bases represent the amino acid valine. A Figure 8.9 The structure of RNA. These three bases represent the amino acid glutamate. If this part of the DNA is being used, a polypeptide chain is made with the amino acid glutamate joined to valine. Figure 8.8 How DNA codes for amino acid sequences in proteins. 128 RNA resembles one polynucleotide strand in DNA, except that the base uracil replaces thymine and the sugar is ribose. Chapter 8: Nucleic acids The sequence of bases on part of a DNA molecule – a gene – is used to build an RNA molecule with the complementary base sequence. This RNA molecule then travels out into the cytoplasm and attaches to a ribosome. Working with other RNA molecules, the base sequence is used to determine the sequence of amino acids that are strung together to make a protein molecule. The base sequence on the DNA therefore determines the primary structure of the protein that is made. SAQ 2 Use a table, or a list of bullet points, to summarise the differences Answer between DNA and RNA. Summary Extension Glossary is deoxyribonucleic acid. It is a double-stranded molecule made up of two strands of •DNA nucleotides. DNA nucleotide is made up of a phosphate group, a five-carbon sugar called deoxyribose, and •Aa base. There are four bases in DNA – adenine, guanine, cytosine and thymine. They are usually abbreviated to A, G, C and T. •Adenine and guanine are purine bases. Cytosine and thymine are pyrimidine bases. nucleotides in a strand of DNA are linked to each other by strong covalent bonds between the •The phosphate groups and deoxyribose. The phosphate groups bond to carbon 5 and to carbon 3 of the deoxyribose ring. The end of the molecule where the phosphate is bonded to carbon 5 is called the 5 end, while the other is the 3 end. two strands of a DNA molecule are linked to each other by weak hydrogen bonds between the •The bases. A always bonds with T, and C always bonds with G. A and T are linked by two hydrogen bonds. C and G are linked by three hydrogen bonds. two strands of a DNA molecule run in opposite directions. They are said to be anti-parallel. •The They twist around each other to form a double helix. DNA molecules in a cell nucleus are replicated before cell division takes place. First, the two •The strands of the molecule are untwisted and unzipped. Free DNA nucleotides pair up with the exposed bases on both strands. They are then linked together by the formation of bonds between their deoxyribose and phosphate groups. This is catalsyed by the enzyme DNA polymerase. Two new molecules are therefore formed, each identical to the original one. Each new molecule contains one old strand and one new strand, so the process is called semi-conservative replication. sequence of bases in a DNA molecule codes for the sequence of amino acids in a protein to be •The made on the ribosomes. Three bases code for one amino acid. A sequence of DNA nucleotides that codes for one polypeptide is known as a gene. is ribonucleic acid. There are several kinds of RNA. Most are single stranded. They contain •RNA the pentose sugar ribose, rather than deoxyribose. They contain the base uracil instead of thymine. protein synthesis, an RNA molecule is built up against one of the DNA strands in a gene. •During The RNA then travels out of the nucleus to a ribosome, where its sequence of bases is used to determine the sequence of amino acids in the polypeptide that is being constructed on the ribosome. 129 Chapter 8: Nucleic acids Questions [3] [1] A B C Figure 1 100 % DNA molecules 1 Figure 1 represents a nucleotide which forms part of a DNA molecule. a i Name A to C. ii State which part of the nucleotide contains nitrogen. During research into the mechanism of DNA replication, bacteria were grown for many generations in a medium containing only the ‘heavy’ isotope of nitrogen, 15N. This resulted in all the DNA molecules containing only 15N. This is illustrated in Figure 2. 75 50 25 0 DNA DNA DNA containing containing containing 14 14 N only N / 15N 15N only Figure 2 The bacteria continued to grow in the ‘light’ nitrogen, 14N, medium until the DNA had replicated once more. The DNA molecules were analysed. The results are shown in Figure 4. Figure 5 shows simple diagrams of DNA molecules, indicating the nitrogen content of each. Key A B C D E F represents DNA with 15N % DNA molecules 100 75 50 25 0 DNA DNA DNA containing containing containing 14 14 N only N / 15N 15N only Figure 3 100 % DNA molecules These bacteria were then grown in a medium containing only ‘light’ nitrogen, 14N. After the time taken for the DNA to replicate once, the DNA was analysed. The results are shown in Figure 3. b Explain how these data support the semi-conservative hypothesis of DNA replication. [3] represents DNA with 15N 75 50 25 0 DNA DNA DNA containing containing containing 14 14 N only N / 15N 15N only Figure 4 Figure 5 100 % DNA molecules c With reference to Figure 5, select the letter or letters which best represent the bacterial DNA in Figure 2, Figure 3 and Figure 4. The bacteria continued to grow in the ‘light’ nitrogen, 14N, medium until the DNA had replicated once more. The DNA molecules were analysed. d Copy and complete the bar chart to the right to indicate the expected results of the composition of these DNA molecules. [3] OCR Biology AS (2801) January 2002 [3] 75 50 25 0 DNA DNA DNA containing containing containing 14 14 N only N / 15N 15N only [Total 13] Answer 130