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Cambridge International AS Level Biology

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Chapter 6:

Nucleic acids and protein synthesis Learning outcomes You should be able to: ■■

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describe the structures of nucleotides and nucleic acids describe the semi-conservative replication of DNA explain how the sequence of nucleotides in DNA codes for the sequence of amino acids in a polypeptide

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explain the roles of DNA and RNA in transcription and translation discuss the effect of gene mutation

Chapter 6: Nucleic acids and protein synthesis

Chemical factories of the future?

All of us – and all other living organisms – have cells that contain DNA. DNA is constructed from a chain of smaller molecules called nucleotides, and the sequence of the bases in these nucleotides acts as a genetic code, determining the proteins that are made in the cell and hence the organism’s characteristics.

The genetic code is universal. It is the same in all organisms.

But recently, the genetic code of a bacterium, Escherichia coli (Figure 6.1), has been deliberately modified. One of the three-letter ‘words’ of its genetic code, which originally told the bacterium’s ribosomes to stop making a protein, has been changed to code for an amino acid that is not found in nature. The new code word now instructs the bacterium to insert the unnatural amino acid into a protein.

These modified bacteria can be made to take up different unnatural amino acids. This means that these bacteria can be used to produce new proteins with specific, unusual properties that could be of use to us. The possibilities are almost endless. For example, a completely new structural protein could be made that is able to bind to a metal, which could be used to build new structures. A new enzyme could be produced that is only active in the presence of another molecule, which could be used as a therapeutic drug to treat human diseases.

The fact that the novel amino acids are not found in nature means that these modified bacteria can only make the new proteins in laboratory conditions, where they are supplied with these amino acids. There is no chance of them surviving if they were to escape into the environment. Nevertheless, our ability to make such fundamental changes to an organism is thoughtprovoking. The chemistry of proteins will look very different in the future.

If you were asked to design a molecule which could act as the genetic material in living things, where would you start?

One of the features of the ‘genetic molecule’ would have to be the ability to carry instructions – a sort of blueprint – for the construction and behaviour of cells and the way in which they grow together to form a complete living organism. Another would be the ability to be copied perfectly, over and over again, so that whenever the nucleus of a cell divides it can pass on an exact copy of each ‘genetic molecule’ to the nuclei of each of its daughter cells.

Until the mid 1940s, biologists assumed that such a molecule must be a protein. Only proteins were thought to be complex enough to be able to carry the huge number of instructions which would be necessary to make such a complicated structure as a living organism. But during the 1940s and 1950s, a variety of evidence came to light that proved beyond doubt that the genetic molecule was not a protein at all, but DNA.

The structure of DNA and RNA

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Figure 6.1 False colour scanning electron micrograph of Escherichia coli (× 1000).

DNA stands for deoxyribonucleic acid, and RNA for ribonucleic acid. As we saw in Chapter 2, nucleic acids such as DNA and RNA, like proteins and polysaccharides, are macromolecules (page 29). They are also polymers, made up of many similar, smaller molecules joined into a long chain. The smaller molecules from which DNA and RNA molecules are made are nucleotides. DNA and RNA are therefore polynucleotides. They are often referred to simply as nucleic acids.

Nucleotides

Figure 6.2 shows the structure of nucleotides. Nucleotides are made up of three smaller components. These are: ■■ ■■ ■■

a nitrogen-containing base a pentose sugar a phosphate group.

Cambridge International AS Level Biology

There are just five different nitrogen-containing bases found in DNA and RNA. In a DNA molecule, there are four: adenine, thymine, guanine and cytosine. An RNA molecule also contains four bases, but never the base thymine. Instead, RNA molecules contain a base called uracil. These bases are often referred to by their first letters: A, T, C, G and U. The pentose (5-carbon) sugar can be either ribose (in RNA) or deoxyribose (in DNA). As their names suggest, deoxyribose is almost the same as ribose, except that it has one fewer oxygen atoms in its molecule.

Figure 6.2 shows the five different nucleotides from which DNA and RNA molecules can be built up.

Figure 6.3 shows the structure of their components in more detail; you do not need to remember these structures, but if you enjoy biochemistry you may find them interesting.

Do not confuse adenine with adenosine, which is part of the name of ATP (adenosine triphosphate) – adenosine is adenine with a sugar joined to it. And don’t confuse thymine with thiamine, which is a vitamin.

P

P

thymine sugar

sugar

P

guanine

cytosine sugar

sugar

P

uracil sugar

Figure 6.2 Nucleotides. A nucleotide is made of a nitrogencontaining base, a pentose sugar and a phosphate group P .

P

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P

adenine

base sugar

nucleotide sugar

P

base

or ribose

O− O

deoxyribose

purine bases

O

−

pyrimidine bases

adenine

O

P

−

CH2OH H H

OH

O

H

H H

OH

CH2OH

OH

OH

O

OH

N

N H

uracil

O

O

NH2

H

H

thymine

H

N

N

H

H N O

H

H

H NH2

O N N

N H

H

H N O

N H

Figure 6.3 The components of nucleotides. Note that you do not need to learn these structural formulae.

H N O

N H

cytosine

guanine

H N NH2

N

CH3 H

H H

H H

Chapter 6: Nucleic acids and protein synthesis

ATP

Although ATP is not part of DNA or RNA, we will look at its structure here because it is very similiar to a nucleotide.

Its structure is shown in Figure 6.4. Adenosine can be combined with one, two or three phosphate groups to give, in turn, adenosine monophosphate (AMP), adenosine diphosphate (ADP) or adenosine triphosphate (ATP).

NH2 N

N O

O– O–

P O

O

P O

–

O– O

P

N O

CH2

O

adenine

N

O ribose

adenosine AMP ADP ATP

Figure 6.4 Structure of ATP.

Polynucleotides

To form the polynucleotides DNA and RNA, many nucleotides are linked together into a long chain. This takes place inside the nucleus, during interphase of the cell cycle (page 97).

Figure 6.5a shows the structure of part of a polynucleotide strand. In both DNA and RNA it is formed of alternating sugars and phosphates linked together, with the bases projecting sideways.

The covalent sugar–phosphate bonds (phosphodiester bonds) link the 5-carbon of one sugar molecule and the 3-carbon of the next. (See Chapter 2 for the numbering of carbon atoms in a sugar.) The polynucleotide strand is said to have 3΄ and 5΄ ends.

DNA molecules are made of two polynucleotide strands lying side by side, running in opposite directions.

The strands are said to be antiparallel. The two strands are held together by hydrogen bonds between the bases (Figure 6.5b and c). The way the two strands line up is very precise.

The bases can be purines or pyrimidines. From Figure 6.3, you will see that the two purine bases, adenine and guanine, are larger molecules than the two

pyrimidines, cytosine and thymine. In a DNA molecule, there is just enough room between the two sugar– phosphate backbones for one purine and one pyrimidine molecule, so a purine in one strand must always be opposite a pyrimidine in the other. In fact, the pairing of the bases is even more precise than this. Adenine always pairs with thymine, while cytosine always pairs with guanine: A with T, C with G. This complementary base pairing is a very important feature of polynucleotides, as you will see later.

DNA is often described as a double helix. This refers to the three-dimensional shape that DNA molecules form (Figure 6.5d). The hydrogen bonds linking the bases, and therefore holding the two strands together, can be broken relatively easily. This happens during DNA replication (DNA copying) and also during protein synthesis (protein manufacture). As we shall see, the breaking of the hydrogen bonds is a very important feature of the DNA molecule that enables it to perform its role in the cell.

RNA molecules, unlike DNA, remain as single strands of polynucleotide and can form very different threedimensional structures. We will look at this later in the chapter when we consider protein synthesis.

DNA replication We said at the beginning of this chapter that one of the features of a ‘genetic molecule’ would have to be the ability to be copied perfectly many times over.

It was not until 1953 that James Watson and Francis Crick (Figure 6.6) used the results of work by Rosalind Franklin (Figure 6.7) and others to work out the basic structure of the DNA molecule that we have just been looking at (Figure 6.8). To them, it was immediately obvious how this molecule could be copied perfectly, time and time again.

Watson and Crick suggested that the two strands of the DNA molecule could split apart. New nucleotides could then line up along each strand, opposite their appropriate partners, and join up to form complementary strands along each half of the original molecule. The new DNA molecules would be just like the old ones, because each base would only pair with its complementary one. Each pair of strands could then wind up again into a double helix, exactly like the original one.

This idea proved to be correct. The process is shown in Figure 6.9 on page 116. This method of copying is called semi-conservative replication, because half of the original molecule is kept (conserved) in each of the new molecules.

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