DNA structure (biology only) — AQA GCSE Biology

A nucleotide is the building block of DNA. Every nucleotide has the same two parts: a sugar molecule called deoxyribose and a phosphate group. Attached to the sugar is one base, and there are four possible bases: adenine (A), cytosine (C), guanine (G) and thymine (T). Because the sugar and phosphate are common to all nucleotides, the four nucleotides differ only in which base is attached. In a DNA strand, the sugar of one nucleotide bonds to the phosphate of the next, forming a repeating sugar-phosphate backbone. The bases project from this backbone and pair with bases on the opposite strand. When describing a nucleotide, always include all three parts: sugar, phosphate and base.

DNA contains four bases, represented by the letters A, C, G and T. These stand for adenine (A), cytosine (C), guanine (G) and thymine (T). The bases are the parts of the nucleotides that carry the genetic code, and their order along a DNA strand determines the sequence of amino acids in a protein. The bases pair in a specific way: A always pairs with T, and C always pairs with G. This complementary base pairing holds the two strands of the double helix together and ensures that DNA can be copied accurately during replication. When answering questions, use the full names as well as the letters, and remember that the letters are the initials of the base names, not the names themselves.

The genetic code is a triplet code: each group of three consecutive bases along a DNA strand specifies one amino acid. During protein synthesis, the DNA template strand is transcribed into a complementary mRNA sequence. For example, the DNA template triplet TAC is transcribed into the mRNA codon AUG, which codes for the amino acid methionine. The ribosome reads each codon in order to assemble the protein. Because there are four bases, there are 4³ = 64 possible triplets, which is more than the 20 amino acids used in proteins, so the code is degenerate: several triplets can code for the same amino acid. Understanding this explains how a gene's base sequence determines the primary structure of a protein, and why a mutation that changes one base can alter a single amino acid and potentially affect protein function.

The linear sequence of bases in a gene determines the linear sequence of amino acids in a polypeptide. During transcription, the DNA base sequence is copied into a complementary mRNA molecule. During translation, the ribosome reads the mRNA codons in order, and transfer RNA molecules bring specific amino acids that are joined by peptide bonds. For example, if the DNA triplet sequence is ATG TTA CGT, the mRNA codons are UAC AAU GCA, and the amino acids are assembled in that exact order. Changing the order of bases changes the order of amino acids, which can alter the protein's shape and function. This explains how genes control cell activity and why mutations can have harmful, neutral or beneficial effects.

A DNA strand is a polymer in which sugar and phosphate groups alternate to form a backbone. Each sugar in the backbone is deoxyribose, and attached to each sugar is one of four bases: adenine (A), thymine (T), cytosine (C) or guanine (G). The bases project from the backbone and form hydrogen bonds with bases on the opposite strand, always A with T and C with G. This arrangement produces the double helix. For example, a short section of one strand might read 5′–phosphate–sugar(A)–phosphate–sugar(T)–phosphate–sugar(G)–3′, with the opposite strand running antiparallel and complementary. The sugar-phosphate backbone gives DNA strength and stability, while the base sequence stores genetic information.

DNA is a polymer built from many repeating monomer units called nucleotides. Each nucleotide has three parts: a phosphate group, a deoxyribose sugar and one of four bases (A, T, C or G). Nucleotides join together in a condensation reaction between the phosphate of one nucleotide and the sugar of the next, forming a sugar-phosphate backbone. The base attached to each sugar can vary, so the sequence of bases along the polymer stores genetic information. For example, a single DNA strand can be represented as a chain of nucleotides, each contributing a sugar, a phosphate and a base. The two strands of a DNA molecule are held together by hydrogen bonds between complementary bases, forming the double helix.

Protein synthesis begins when a gene's DNA base sequence is copied into a messenger molecule, which carries the code to a ribosome. There, the bases are read in triplets, and each triplet specifies an amino acid; the amino acids are joined in order to form a protein. The DNA base sequence therefore determines the amino acid sequence, which determines how the protein folds and functions. A genetic variant is a change in the DNA base sequence. In coding DNA, a variant can change the amino acid sequence, altering the protein's activity, for example changing an enzyme's active site so it no longer works. In non-coding DNA, a variant can alter how genes are expressed, for example by changing whether a gene is switched on or off, which changes the amount of protein made and so affects phenotype.

DNA is a double-stranded molecule held together by hydrogen bonds between bases on opposite strands. The strands are complementary, meaning the base on one strand determines the base on the other. Cytosine (C) always pairs with guanine (G), and thymine (T) always pairs with adenine (A). This is called complementary base pairing. Because of this rule, if you know the sequence of one strand, you can work out the sequence of the other. For example, if one strand reads A T G C, the opposite strand reads T A C G. The pairing also explains Chargaff's observation that the amount of A equals the amount of T, and the amount of C equals the amount of G in double-stranded DNA.

A change in DNA structure means a change in the base sequence of a gene. Because the base sequence is read in sets of three to specify amino acids, altering it can change the amino acids inserted into the protein. A substitution may change one amino acid, while an insertion or deletion can shift the reading frame so that many amino acids after the change are different. The altered amino acid sequence can change how the protein folds, which may change its shape and therefore its function. For example, a changed active site may no longer bind its substrate. The result is a different protein synthesised by that gene, which may affect the phenotype.

Protein synthesis occurs on ribosomes, which are the cell's protein factories. The template is a molecule of messenger RNA (mRNA) that carries a copy of the gene's base sequence from the DNA in the nucleus to the ribosome. The ribosome binds to the mRNA and reads its bases in groups of three (codons). Each codon specifies one amino acid. Transfer RNA (tRNA) molecules bring the correct amino acids to the ribosome, where they are joined in the order dictated by the mRNA codons. In this way, the base sequence of the gene determines the amino acid sequence of the protein. For example, the codon AUG on mRNA codes for the amino acid methionine, so the ribosome will place methionine at the start of the protein chain. The process is called translation.

In protein synthesis, carrier molecules play a vital role in ensuring the correct amino acids are assembled. Once a template of the DNA code is produced and moves to the ribosome, carrier molecules bring specific amino acids to add to the growing protein chain. Each carrier molecule is specific to one type of amino acid and recognises a specific sequence of three bases on the template. During translation at the ribosome, the carrier molecules align in the correct order dictated by the template. This ensures that the amino acids are joined together in the precise sequence required to fold into a functional protein. Once an amino acid is added to the chain, the carrier molecule is released and can be reused.

After translation, the polypeptide chain is complete but not yet functional. It must fold into a specific three-dimensional shape. This folding is determined by the sequence of amino acids, which dictates interactions such as hydrogen bonds, ionic bonds, disulfide bridges and hydrophobic interactions between different parts of the chain. The unique shape is crucial for the protein's function. For example, enzymes have an active site that is complementary to their substrate; this shape is a result of folding. If the protein does not fold correctly, it may be non-functional. The folding process can occur spontaneously or with the help of chaperone proteins. The final shape is often described as the protein's tertiary structure.

When a protein chain is assembled, it folds up into a unique three-dimensional shape. This unique shape is essential because it enables the protein to carry out its specific function in the body. For example, enzymes fold to create a specific active site that is complementary to a particular substrate, allowing them to catalyse chemical reactions. Hormones, such as insulin, rely on their specific shape to bind to target receptors and trigger responses. Structural proteins, like collagen, form strong, fibrous shapes that provide structural support in tissues such as skin and bone. If the unique shape of a protein is altered, for instance by extreme temperatures causing denaturation, the protein will lose its ability to function.

Mutations are random changes in the base sequence of DNA that happen continuously, including during DNA replication before cell division. Because the genetic code is degenerate and many amino acids have more than one codon, a base substitution often still codes for the same amino acid, so the primary structure and therefore the folded protein are unchanged. Even when a different amino acid is inserted, it may sit in a region that is not critical for the protein's shape or activity, so the appearance or function is only slightly altered or unaffected. For example, a substitution in a gene for an enzyme may change an amino acid far from the active site, leaving the substrate binding site unchanged and the enzyme still functional. Only a minority of mutations produce a protein with a markedly different shape or function.

A mutation changes the base sequence of DNA, which can change the sequence of amino acids in the protein made during translation. Because a protein's shape is determined by the sequence and interactions of its amino acids, a change in amino acid sequence can alter the way the polypeptide folds. A few mutations therefore code for an altered protein with a different shape. For example, a substitution that changes an amino acid in the active site of an enzyme can change the shape of the active site so that the substrate no longer fits. The effect may be harmful, neutral or occasionally beneficial, but the key idea is that a changed amino acid sequence can produce a changed three-dimensional shape and therefore a changed function.

When a mutation changes the amino acid sequence of a protein, the protein may fold into a different shape. If the protein is an enzyme, the shape of its active site may change so that the substrate no longer fits and the enzyme cannot catalyse the reaction. This is described as the substrate binding site no longer fitting the substrate. If the protein is a structural protein, such as collagen in connective tissue or keratin in skin, hair and nails, a changed shape can reduce its strength or alter its function. For example, a mutation in a gene for collagen could produce collagen fibres that are weaker, affecting the strength of tissues. The effect depends on the role of the protein and where the changed amino acids are located.

DNA contains many base sequences, but only some of them code for proteins. A gene is a sequence of DNA that codes for a particular protein, but between genes there are non-coding regions. Even within a gene, not all bases necessarily code for amino acids; there are non-coding sections such as introns in eukaryotes. These non-coding parts of DNA do not directly determine the amino acid sequence of a protein. They can have roles in regulating gene expression, for example controlling whether a gene is switched on or off, and some non-coding DNA is involved in the structure of chromosomes. Mutations in non-coding DNA may therefore have no effect on a protein, or may affect how genes are expressed.

Not all parts of a DNA molecule code for proteins. The non-coding parts of DNA play a crucial role in regulating gene expression by switching genes on and off. This means they control whether a specific gene is used to produce a protein. Because these switches are made of DNA bases, variations or mutations in these non-coding areas can affect how genes are expressed. For example, a mutation in a non-coding region might prevent a gene from being switched on, reducing the amount of a specific protein produced, even though the gene's actual coding sequence remains completely unchanged. This explains why variations in non-coding DNA can significantly alter an organism's phenotype without changing the structure of the proteins themselves.