In Chapter 2: Maintaining a balance we introduced the four major biomolecules contained in cells. These were nucleic acids (DNA/RNA), proteins, lipids, and carbohydrates. These each have distinct structural and biochemical properties that lend to their individual functions within the cell. Table 6.1 outlines some of these features for you. Collectively, they create the molecular players, structures, and organelles that perform tasks within the cell. In this chapter, we will look more closely at the nucleic acids and their role in synthesising another of the biomolecules: proteins.

6.1 | What is the genetic code?

The nucleic acid family of molecules includes deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic code that serves as a blueprint for the transfer of information within the cell. During the lifespan of an individual cell, the information stored within DNA sequences will determine which RNA coding is produced and ultimately which protein sequences are generated by the cell (Figure 6.1). This is known as the “central dogma of genetics”.

As the story starts with DNA and RNA let us first briefly examine their structure. The monomer unit (or repeating unit) that is used to build nucleic acids is called a nucleotide.

Each nucleotide has three distinct components: a nitrogenous base, five-carbon sugar, and a phosphate group (Figure 6.2).

• Nitrogenous bases are broken down into two families, including pyrimidines with a one-ringed structure (thymine (T), cytosine (C), and uracil (U)) and purines with a two-ringed structure (adenine (A) and guanine (G)) (Figure 6.3). DNA is coded by ATCG nucleotides whereas RNA uses AUCG, exchanging U in place of T.
• The five-carbon sugar can either be deoxyribose (for DNA only) or ribose (for RNA only). (See next chapter for structure of different sugars).
• The phosphate group is a phosphorous atom attached to four oxygen atoms.

Nucleotides assemble to form long strands of the nucleic acids DNA or RNA. The DNA strand can be visualised as a chain consisting of a sugar phosphate backbone with bases sticking out at regular intervals from it (Figure 6.3).

Nucleic acid strands can also form weaker associations to other nucleic acid strands through hydrogen bonding between the nitrogenous bases. Due to the structure and biochemical nature of each nucleotide, only complementary base pairing can occur. This includes A bonding with T and C bonding with G.

In nature, DNA only occurs in the form of two complementary DNA strands. Two DNA strands arranged in anti-parallel configuration as shown in Figures 6.3 and 6.4. The two DNA chains are complementary, that is A on one chain will hydrogen bond with the T on the other, whereas the C on one chain will hydrogen bond with G on the other. Note that scientists discovered that the two complementary strands did not just exist in straight strands but formed the helical structure known as the double helix (Figure 6.4).

Note that the RNA strand can also be visualised as a chain with a sugar-phosphate backbone with bases sticking out at regular intervals, except that the base T is replaced with the base U (Figure 6.5).

6.2 | Why is DNA confined to the nucleus?

The nucleus is the largest and most prominent of a cell’s organelles (Figure 6.6). The nucleus is generally considered the control centre of the cell because it stores all of the genetic instructions for manufacturing proteins. Interestingly, some cells in the body, such as skeletal muscle cells, contain more than one nucleus (Figure 6.7); a skeletal muscle cell is termed multinucleate. Other cells, such as mammalian red blood cells (RBCs), do not contain nuclei at all. RBCs eject their nuclei as they mature, making space for the large numbers of haemoglobin molecules that carry oxygen throughout the body. Without nuclei, the life span of RBCs is short, and so the body must produce new ones constantly.

Inside the nucleus lies the blueprint that dictates everything a cell will do and all of the products it will make. This information is stored within DNA. The nucleus sends commands to the cell via molecular messengers that translate the information from DNA. Each cell in your body (with the exception of reproductive cells and red blood cells) contains the complete set of your DNA. However, when cells become specialised some genes are turned off as necessary for their function.

Like most other cellular organelles, the nucleus is surrounded by a membrane called the nuclear envelope. This membranous covering consists of two adjacent lipid bilayers with a thin fluid space in between them. Spanning these two bilayers are nuclear pores. A nuclear pore is a tiny passageway for the passage of proteins, RNA, and solutes between the nucleus and the cytoplasm. DNA molecules are far too large to go through these pores (Figure 6.8)

Inside the nuclear envelope is a gel-like nucleoplasm with solutes that include the building blocks of nucleic acids. There also can be a dark-staining mass often visible under a simple light microscope, called a nucleolus. As we learnt in Chapter 2: Maintaining a balance, the nucleolus is a region of the nucleus that is responsible for manufacturing the RNA necessary for construction of ribosomes. Once synthesised, newly made ribosomal subunits exit the cell’s nucleus through the nuclear pores. These ribosomes attach to sections of the endoplasmic reticulum to give it a studded appearance (refer to Chapter 2: Maintaining a balance).

The genetic instructions that are used to build and maintain an organism are arranged in an orderly manner in strands of DNA. Within the nucleus are threads of chromatin composed of DNA and associated proteins (Figure 6.8). Along the chromatin threads, the DNA is wrapped around a set of histone proteins.  A nucleosome is a single, wrapped DNA-histone complex. Multiple nucleosomes along the entire molecule of DNA appear like a beaded necklace, in which the string is the DNA and the beads are the associated histones. When a cell is in the process of division, the chromatin condenses into chromosomes, so that the DNA can be safely transported to the daughter cells. The chromosome is composed of DNA and proteins; it is the condensed form of chromatin. It is estimated that humans have almost 22,000 genes distributed on 46 chromosomes.

How does DNA copy itself?

For an organism to grow, develop, and maintain its health, cells must reproduce themselves by dividing to produce two new daughter cells, each with the full complement of DNA as found in the original cell. Billions of new cells are produced in an adult human every day.  The division time of different cell types varies. Epithelial cells of the skin and gastrointestinal lining, for instance, divide very frequently to replace those that are constantly being rubbed off of the surface by friction.

The particular sequence of bases along the DNA molecule determines the genetic code. Due to complementary base pairing, if the two strands of DNA were pulled apart, you could infer the order of the bases in one strand from the bases in the other, complementary strand. For example, if one strand has a region with the sequence AGTGCCT, then the sequence of the complementary strand would be TCACGGA.

DNA replication is the copying of DNA that occurs before cell division can take place. After a great deal of debate and experimentation, the general method of DNA replication was deduced in 1958 by two scientists in California, Matthew Meselson and Franklin Stahl. This method is illustrated in Figure 6.9 and occurs in three stages as described below. Note that several enzymes take part in DNA replication and that the suffix “ase” is used to denote an enzyme

Each new DNA molecule contains one strand from the original molecule and one newly synthesised strand. Semiconservative is the term for this mode of replication, because half of the original DNA molecule is conserved in each new DNA molecule. This process continues until the cell’s entire genome, the entire complement of an organism’s DNA, is replicated. As you might imagine, it is very important that DNA replication take place precisely so that new cells in the body contain the exact same genetic material as their parent cells. Mistakes made during DNA replication, such as the accidental addition of an inappropriate nucleotide, have the potential to render a gene dysfunctional or useless. Fortunately, there are mechanisms in place to minimise such mistakes. A DNA proofreading process enlists the help of special enzymes that scan the newly synthesised molecule for mistakes and corrects them. Once the process of DNA replication is complete, the cell is ready to divide.

6.3 | How does the body use the genetic code?

It was mentioned earlier that DNA provides a blueprint for the cell structure and physiology. This refers to the fact that DNA contains the information necessary for the cell to build one very important type of molecule: the protein. Most structural components of the cell are made up, at least in part, by proteins and virtually all the functions that a cell carries out are completed with the help of proteins. One of the most important classes of proteins is enzymes, which help speed up necessary biochemical reactions that take place inside the cell. Some of these critical biochemical reactions include building larger molecules from smaller components (such as occurs during DNA replication) and breaking down larger molecules into smaller components (such as when harvesting chemical energy from nutrient molecules). Whatever the cellular process may be, it is almost sure to involve proteins.

Protein synthesis begins with genes. A gene is a functional segment of DNA that provides the genetic information necessary to build a protein. Each particular gene provides the code necessary to construct a particular protein. Gene expression, which transforms the information coded in a gene to a final gene product, ultimately dictates the structure and function of a cell by determining which proteins are made.

The interpretation of genes works in the following way. Recall that proteins are polymers, or chains, of many amino acid building blocks. The sequence of bases in a gene (that is, its sequence of A, T, C, G nucleotides) translates to an amino acid sequence. A triplet is a section of three DNA bases in a row that codes for a specific amino acid. Similar to the way in which the three-letter code d-o-g signals the image of a dog, the three-letter DNA base code signals the use of a particular amino acid. For example, the DNA triplet CAC (cytosine, adenine, and cytosine) specifies the amino acid valine. Therefore, a gene, which is composed of multiple triplets in a unique sequence, provides the code to build an entire protein, with multiple amino acids in the proper sequence (Figure 6.10). The mechanism by which cells turn the DNA code into a protein product is a two-step process, with an RNA molecule as the intermediate.

Step 1: From DNA to RNA: Transcription

DNA is housed within the nucleus, and protein synthesis takes place in the cytoplasm, thus there must be some sort of intermediate messenger that leaves the nucleus and manages protein synthesis. This intermediate messenger is messenger RNA (mRNA), a single-stranded nucleic acid that carries a copy of the genetic code for a single gene out of the nucleus and into the cytoplasm where it is used to produce proteins.

There are several different types of RNA, each having different functions in the cell. The structure of RNA is similar to DNA with a few small exceptions. For one thing, unlike DNA, most types of RNA, including mRNA, are single-stranded and contain no complementary strand. Second, the ribose sugar in RNA contains an additional oxygen atom compared with DNA. Finally, instead of the base thymine, RNA contains the base uracil. This means that adenine will always pair up with uracil during the protein synthesis process.

Gene expression begins with the process called transcription, which is the synthesis of a strand of mRNA that is complementary to the gene of interest. This process is called transcription because the mRNA is like a transcript, or copy, of the gene’s DNA code. Transcription begins in a fashion somewhat like DNA replication, in that a region of DNA unwinds and the two strands separate, however, only that small portion of the DNA will be split apart. The triplets within the gene on this section of the DNA molecule are used as the template to transcribe the complementary strand of RNA (Figure 6.11). A codon is a three-base sequence of mRNA, so-called because they directly encode amino acids. The four different bases (A, T, C & G) can combine in 64 unique combinations (Table 6.2). 61 of these code for the 20 amino acids that the body can make, while the other 3 are termination (STOP) signals (UAA, UAG & UGA).

Step 2: From RNA to protein: Translation

Like translating a book from one language into another, the codons on a strand of mRNA must be translated into the amino acid alphabet of proteins. Translation is the process of synthesising a chain of amino acids called a peptide, which is what the larger protein molecules are made of. Translation requires two major aids: first, a “translator,” the molecule that will conduct the translation, and second, a specific place where the mRNA strand is translated into a new protein, like the translator’s “desk.” Both of these requirements are fulfilled by other types of RNA. The “desk” on which translation takes place is the ribosome. The ribosome provides a place for translation, bringing together and aligning the mRNA molecule with the molecular “translators” that must decipher its code.

The other major requirement for protein synthesis is the translator molecules that physically “read” the mRNA codons. Transfer RNA (tRNA) is the translator; it is a type of RNA that transports the appropriate corresponding amino acids to the ribosome, and attaches each new amino acid to the last, building the peptide chain one by one. Thus tRNA transfers specific amino acids from the cytoplasm to a growing polypeptide. The tRNA molecules must be able to recognise the codons on mRNA and match them with the correct amino acid. The tRNA is modified for this function. On one end of its structure is a binding site for a specific amino acid. On the other end is a base sequence that matches the codon specifying its particular amino acid. This sequence of three bases on the tRNA molecule is called an anticodon. For example, a tRNA responsible for shuttling the amino acid glycine contains a binding site for glycine on one end. On the other end it contains an anticodon that complements the glycine codon (GGA is a codon for glycine, and so the tRNAs anticodon would read CCU). Equipped with its particular cargo and matching anticodon, a tRNA molecule can read its recognised mRNA codon and bring the corresponding amino acid to the growing chain (Figure 6.12).

Much like the processes of DNA replication and transcription, translation also consists of three main stages: initiation, elongation, and termination. Initiation takes place with the binding of a ribosome to an mRNA transcript. The elongation stage involves the recognition of a tRNA anticodon with the next mRNA codon in the sequence. Once the anticodon and codon sequences are bound (remember, they are complementary base pairs), the tRNA presents its amino acid cargo and the growing polypeptide strand is attached to this next amino acid. This attachment takes place with the assistance of various enzymes and requires energy. The tRNA molecule then releases the mRNA strand, the mRNA strand shifts one codon over in the ribosome, and the next appropriate tRNA arrives with its matching anticodon. This process continues until the final codon on the mRNA is reached which provides a “stop” message that signals termination of translation and triggers the release of the complete, newly synthesised protein.  Thus, a gene within the DNA molecule is transcribed into mRNA, which is then translated into a protein product (Figure 6.13). Note that polypeptides are larger than peptides and proteins are larger than polypeptides but all have amino acids as their main building blocks.

Commonly, an mRNA transcription will be translated simultaneously by several adjacent ribosomes. This increases the efficiency of protein synthesis. A single ribosome might translate an mRNA molecule in approximately one minute; so multiple ribosomes aboard a single transcript could produce multiple times the number of the same protein in the same minute.

6.4 | How do proteins get their 3-dimensional structure?

As we discussed earlier, a protein’s shape is critical to its function. For example, an enzyme can bind to a specific substrate at an active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.

Primary structure

The unique sequence and number of amino acids in a polypeptide chain is its primary structure (Figure 6.14). The unique sequence for every protein is ultimately determined by the gene that encodes the protein.

Secondary structure

Folding patterns resulting from interactions between the non-R group portions of amino acids give rise to the secondary structure of the protein (Figure 6.15). The most common are the alpha (α)-helix and beta (β)-pleated sheet structures. Both structures are held in shape by hydrogen bonds. In the alpha helix, the bonds form between every fourth amino acid and cause a twist in the amino acid chain.

Tertiary structure

The unique three-dimensional structure of a polypeptide is known as its tertiary structure (Figure 6.14). This structure is caused by chemical interactions between various amino acids and regions of the polypeptide. Primarily, the interactions among R groups create the complex three-dimensional tertiary structure of a protein. There may be ionic bonds formed between R groups on different amino acids, or hydrogen bonding beyond that involved in the secondary structure. When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, whereas the hydrophilic R groups lay on the outside.

Quaternary structure

In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between the subunits help to stabilise the overall structure. For example, haemoglobin is a combination of four polypeptide subunits (Figure 6.14).

How is the function of a protein disrupted if its structure changes?

Each protein has its own unique sequence and shape held together by chemical interactions. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape three-dimensional shape in what is known as denaturation. Denaturation is often reversible because the primary structure is preserved if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to a loss of function. One example of protein denaturation can be seen when an egg is fried or boiled. The albumin protein in the liquid egg white is denatured when placed in a hot pan, changing from a clear substance to an opaque white substance. Not all proteins are denatured at high temperatures, it will depend on the natural environment for the particular protein; for instance, bacteria that survive in hot springs have proteins that are adapted to function at those temperatures.

6.5 | What happens if there is a mistake in the DNA?

A mutation is a heritable change in the DNA sequence of an organism. The resulting organism may have a recognisable change in function compared to the original. A change in the DNA sequence will be copied to mRNA through transcription and may lead to an altered amino acid sequence during translation. Because proteins carry out the vast majority of cellular functions, a change in amino acid sequence in a protein may lead to an altered function for the cell and organism.

Effects of mutations on DNA sequence

There are several types of mutations that are classified according to how the DNA molecule is altered. One type, called a point mutation, affects a single base and most commonly occurs when one base is substituted or replaced by another. Mutations also result from the addition of one or more bases, known as an insertion, or the removal of one or more bases, known as a deletion. Mutations which cause the insertion or deletion of bases in less than multiples of 3 cause the most change in the amino acid sequence because they result in a frameshift. This means that all bases following the frameshift will be incorrect. Consequentially, proteins made from genes containing frameshift mutations are nearly always non-functional.

Effects of mutations on protein structure and function

Point mutations may have a wide range of effects on protein function. Because there are 61 codon combinations and only 20 amino acids, there is a chance that a point mutation in a gene sequence will result in the same amino acid being incorporated into the resulting polypeptide despite the sequence change. This change would have no effect on the protein’s structure and is thus called a silent mutation.

If a different amino acid is incorporated then the final structure of the protein may be compromised, meaning that it may not be able to perform its function. This depends on many factors, such as how different the chemical properties of the two amino acids are, and where in the sequence the change has happened. For example, if the change happened in an enzyme’s active site, then the substrate may no longer fit.

An example of a genetic mutation

Any change in the gene sequence may lead to a different amino acid being added to the polypeptide chain, causing a change in protein structure and function. In sickle cell anaemia, the haemoglobin β chain has a single amino acid substitution (Figure 6.15), causing a change in both the structure and function of the protein. What is most remarkable to consider is that a haemoglobin molecule is made up of two alpha chains and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal haemoglobin molecule and a sickle cell molecule—that dramatically decreases life expectancy in the affected individuals—is a single amino acid of the 600. What is even more remarkable is that three nucleotides each encode those 600 amino acids, and a single base change (point mutation), 1 in 1800 bases causes the mutation.

Because of this change of one amino acid in the chain, haemoglobin molecules form long fibres that distort the biconcave, or disc-shaped, red blood cells and causes them to assume a crescent or “sickle” shape, which clogs blood vessels (Figure 6.16). This can lead to myriad serious health problems such as breathlessness, dizziness, headaches, and abdominal pain for those affected by this disease.

Chapter attribution

Content adapted from:

Chapter 3.4 Protein Synthesis in Anatomy and Physiology 2e (2022) by J. Gordon Betts, Kelly A. Young, James A. Wise, Eddie Johnson, Brandon Poe, Dean H. Kruse, Oksana Korol, Jody E. Johnson, Mark Womble and Peter DeSaix is published by OpenStax, https://openstax.org/details/books/anatomy-and-physiology-2e, and used under a CC BY licence.

Chapter 3.4 Proteins in Biology 2e (2018) by Mary Ann Clark, Matthew Douglas and Jung Choi is published by OpenStax, https://openstax.org/details/books/biology-2e, and used under a CC BY licence.

Concepts of Biology (2013), by Samantha Fowler, Rebecca Roush and James Wise, is published by OpenStax https://openstax.org/details/books/concepts-biology, and used under a CC BY licence.

Chapter 11.5 Mutations in Microbiology (2016) by Nina Parker, Mark Schneegurt, Anh-Hue Thi Tu, Philip Lister and Brian M. Forster is published by OpenStax, https://openstax.org/details/books/microbiology, and used under a CC BY licence.