The third part of this series looks at proteins and mutations
Alyson Bexfield, PhD, BSc, is senior research assistant; Yamni Nigam, PhD, BSc, MSc, is lecturer, Centre for Biomedical Studies; both at School of Health Science, Swansea University.
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Genes: the blueprint for proteins
Proteins are an important class of molecules in living organisms, making up 50% of the mass of most cells (excluding water). They are made up of units called amino acids, and have important and diverse functions, including oxygen transport in red blood cells (haemoglobin), formation of hair and fingernails (keratin), movement (muscle proteins called actin and myosin) and immunity (antibodies).
Enzymes, another type of protein, are particularly important as they catalyse and regulate chemical reactions in the body, from DNA replication to digestion of food in the gut. In fact, proteins are necessary for virtually every activity in the body.
How are proteins made?
As mentioned in articles 1 and 2 of this series, genes contain the information necessary to make proteins. There are two major types of genes - structural and regulatory (Seeley et al, 2008).
- Structural genes determine specific amino acid sequences in proteins.
- Regulatory genes are segments of DNA involved in controlling which structural genes are expressed, or ‘switched on’, in a given tissue.
By determining the structure of proteins and regulating which are produced by cells, genes are responsible for the characteristics of cells, and therefore the inherited characteristics, or traits, of the entire organism (Seeley et al, 2008).
The conversion of DNA into proteins is known as protein synthesis or gene expression. This process takes place in ribosomes in the cytoplasm of cells (Fig 1), and involves two main steps:
- Transcription of DNA to ribonucleic acid (RNA);
- Translation of RNA into proteins.
DNA usually exists as two polynucleotide strands, coiled into a helix (see article 2). Each strand is a chain of four types of nucleotide - adenine (A), guanine (G), cytosine (C) and thymine (T). The two polynucleotide strands are not identical, they are complementary to each other.
For the synthesis of proteins, only one strand, the coding strands is used. The information encoded in the nucleotides of a DNA molecule (the genetic code) specifies the sequence of building blocks (amino acids) that result in a protein (polypeptide).
DNA is too big (and too important) to travel out of the nucleus, so it enlists the help of another smaller molecule, RNA. This exists in three forms - messenger (mRNA), transfer (tRNA) and ribosomal (rRNA). All three are critical in the manufacture of proteins (Marieb, 2000).
RNA is very similar to DNA, although the pentose sugars that make up part of its structure are different and the nucleotide thymine (T) is replaced with another called uracil (U).
The RNA that carries the genetic code to the ribosomes is messenger RNA (mRNA). In a similar fashion to that of DNA replication (see article 2), the coding DNA strand acts as a template and is copied to produce a complementary strand of RNA, in which A binds with U and G binds with C (Fig 2). The mRNA molecule leaves the nucleus and moves into the cytoplasm where it attaches to a ribosome and acts as a template for the synthesis of a protein.
Where a DNA molecule has many genes and codes for many proteins, each mRNA molecule is a copy of only one gene and codes for only one protein (Montague et al, 2005). The message in the mRNA is ‘translated’ into the language of proteins (amino acids) using the genetic code.
The sequence of nucleotides in a DNA molecule is divided into sets of three, known as triplets, which form ‘words’ of the triplet code. Just as the sequence of letters ‘seedogrun’ can be deciphered as ‘see dog run’, a sequence of bases, such as ‘CATGAGTAG’, has meaning, which is used to construct other molecules or proteins (Seeley et al, 2008).
The corresponding three-base sequences on mRNA are called codons. Each triplet codes for a particular amino acid. For example, the DNA triplet AAA codes for phenylalanine, while CCT codes for glycine. Many triplets are arranged (along with some non-coding regulatory sections of DNA) into genes. There are 64 possible triplet combinations of A, T, G and C, however, only 20 naturally occurring amino acids are found in proteins. Therefore, multiple triplets encode the same amino acid.
There are four codons that do not encode amino acids but control when translation (and formation of the polypeptide chain) will start (AUG), and stop (UAA, UAG, UGA).
Translation of mRNA into polypeptides requires tRNA - short sections of RNA that have binding sites for individual amino acids. Each type of amino acid has its own specific tRNA.
Transfer RNA molecules dock into ribosomes, the site of protein synthesis, and align the correct amino acid to the correct codon. This ensures that the protein being synthesised has the amino acids in the correct order and will therefore be able to function properly. Enzymes then connect the amino acids to form a polypeptide chain. When this is completed it is released from the ribosome and folds into its active form (Fig 1). Thus a protein has been made.
Protein synthesis can be illustrated using the following analogy (Seeley et al, 2008). Suppose a chef wants a cake recipe that is found only in a reference book in the library. Because the book cannot be taken out, the chef makes a copy (transcription) of the recipe. In the kitchen, the chef translates the information in the copied recipe using raw ingredients brought to the kitchen by assistants and a cake is made.
In this analogy, DNA is the reference book that contains many recipes (genes) for different proteins. Just as the book stays in the library, DNA remains in the nucleus. Therefore, through transcription, the cell makes an mRNA copy of the gene necessary to make a particular protein.
This copy travels from the nucleus to ribosomes in the cytoplasm, where the information is used in order to construct a protein (the gene is translated). The raw ingredients necessary to synthesise a protein are amino acids. Specialised transport molecules, tRNA, carry the amino acids to the ribosomes, where rRNA aids the construction of the protein.
Cells depend on thousands of proteins to function correctly. However, DNA can be damaged and mutated in many ways. A mutation that alters a protein that plays a critical role can result in a medical condition. A condition caused by mutations in one or more genes is called a genetic disorder. Luckily, only a small percentage of mutations cause genetic disorders and most have no impact on health.
Problems occur when the correct amino acid(s) are not added to the growing polypeptide chain. In a string of nucleotides within a DNA molecule, a coding triplet is defined from the initial nucleotide from which translation starts. As there are three nucleotides in each triplet, every DNA sequence can be read in three different ways (called reading frames). For example, the DNA sequence AATTGGCCT can be read in the three frames:
AAT TGG CCT: leucine, threonine, glycine;
A ATT GGC CT: stop, proline;
AA TTG GCC T: asparagine, arginine.
The three different frames would encode very different amino acids and proteins. If the first resulted in the desired protein, the proteins produced by the other two would be non-functional.
Changes in DNA caused by mutations can cause errors in the amino acid sequence, creating partially or completely non-functional proteins (Montague et al, 2005). The most common mistake involves the substitution of a single nucleotide, and is known as a point mutation. Depending on its position, this may be insignificant or change the amino acid encoded and possibly the properties of the resultant protein, such as how well it folds into its active form. Point mutations can be:
Silent (encode the same amino acid);
Missense (encode a different amino acid - this type of mutation is responsible for sickle-cell anaemia and cystic fibrosis);
Nonsense (encode a ‘stop’ and shorten the protein, as in example 2 above).
More serious mutations involve the addition or deletion of a single nucleotide or sequence of nucleotides.
Mutations can be divided into germ-line mutations (in the gametes), which can transmit hereditary diseases, and somatic mutations, which are not hereditary. Some mutations can cause cells to become malignant and cancerous. The effects of mutations and other genetic disorders are discussed in article 4.
Marieb, E.N. (2000) Essentials of Human Anatomy and Physiology. San Francisco, CA: Benjamin Cummings.
Montague, S.E. et al (2005) Physiology for Nursing Practice (3rd ed). New York, NY: Elsevier.
Seeley, R. et al (2008) Anatomy and Physiology (3rd ed). New York, NY: McGraw Hill.