Amino Acids - Why They Matter Trivia Quiz

Answer: It allows protein structure and function to be probed

Alanine is chemically simple and so by replacing other amino acids of a protein with alanine, it may be deduced what role these replaced residues play (either functionally or structurally). For example, glutamate, which usually exists as a negatively charged form, may be involved in a charge-charge interaction with a positively charged residue (arginine, for example). If there is indeed a charge-charge interaction, and if this interaction has any significance in either the structure or the function of the protein, this will be apparent following alanine mutagenesis, since alanine is incapable of mimicking the negative charge of glutamate.

Alanine is also one of the most important amino acids in gluconeogenesis - the process of synthesising glucose from non-carbohydrate sources in times of starvation/intense exercise. In active muscles, pyruvate is released when glucose is metabolised. This pyruvate can be converted back to glucose in the liver, but is unable to travel in the blood. Pyruvate is therefore either converted in the muscle into lactate or alanine, which are then transported to the liver via the blood, where they are converted to glucose. When carried as lactate, this is known as the Cori cycle, and when carried as alanine, it is the alanine cycle.

Answer: Tyrosine

Phenylalanine is rather boringly, yet conveniently, named for the fact that it is essentially an alanine with a phenyl group (benzene) attached. When this phenyl group is hydroxylated, it becomes tyrosine, and further modification can yield neurotransmitters and hormones such as dopamine, noradrenaline, and adrenaline, which exhibit important and complex functions in the brain and other areas of the body. Phenylalanine is classed as an essential amino acid (i.e. we obtain it from our diet), but the reactions touched upon above are all carried out by enzymes in our body. That being said, some people lack the enzyme required to convert phenylalanine to tyrosine.

These people have a condition known as phenylketonuria and their consumption of food and drink high in phenylalanine can cause health problems and even death. Perhaps the best known example of this is Coca-Cola, which now adds warning labels that their product may contain a source of this amino acid.

Answer: Because histidine can act as both an acid and a base

The Bronsted-Lowry definition of an acid is a proton donor. The equivalent definition of a base is a proton acceptor. Histidine can act as both. But aren't acids and bases polar opposites? The vague and perhaps disappointing answer is that it is all relative. To be more specific, it is all relative to physiological pH (around 7). Amino acid side chains can be assigned a value known as a pKa, which tells us about whether they act as an acid or as a base. If the pKa of an amino acid side chain is higher than the physiological pH, it is a base. If the pKa of an amino acid side chain is lower than the physiological pH, it is an acid. Histidine's side chain has a pKa value close to physiological pH, meaning that it is granted flexibility in its proton donation and acceptance. Proton exchange is a common feature of the chemistry that takes place at the active sites of many enzymes and so, therefore, is histidine.

A second interesting feature of histidine (and one that has been invaluable to biological research) is its ability to bind metals, particularly zinc. Various research groups are interested in one type of protein only, and so may wish to isolate their pet protein in order to study it more closely. One way of doing this is to alter the gene which codes for the protein with an aim of incorporating several histidine residues at the terminus of the protein. For reasons that are self-explanatory, this is called a poly-histidine tail. Cells producing this protein will also produce many other proteins. These cells can be broken open and the lysate passed over a column to which zinc is attached. Due to zinc's affinity for histidine, the target protein will remain in the column whilst other proteins wash out.

Answer: ATP synthase Fo

ATP synthase is located in the inner mitochondrial membrane and is unlikely to come into contact with DNA in normal circumstances.

Protein-DNA interactions are important in regulating chromatin packing (e.g. histones), DNA replication, and gene transcription (e.g. CAP and transcription factor IIB). Arginine's guanidium group tends to bind AT-rich regions and is (by far) the most enriched amino acid at DNA-binding domains of proteins. At a basic level, this is unsurprising, considering that DNA is negatively charged (owing to its phosphate groups). Arginine is also useful in binding DNA since it is able to both accept and donate hydrogen bonds. Amino acids form hydrogen bonds at the Hoogsteen edge of nucleotide base (the "top" edge of the nucleotides as they are usually drawn). DNA is arranged in such a way as to have a major groove and a minor groove. In its most common form (the B-form) DNA's nucleotide sequence is distinct in the major groove, but is ambiguous in the minor groove. Proteins which bind to DNA in a nucleotide-sequence-specific manner therefore must bind via the major groove (though interactions with the minor groove may also occur to increase binding affinity).

Answer: Huntington's disease

The gene coding for what is known as the Huntington protein is located on chromosome 4 in the human genome. The function of this protein is ambiguous, but the observation that the number of consecutive glutamines in this protein is linked to the development of Huntington's disease is undeniable. The gene coding for the Huntington protein contains a chain of CAG repeats (which codes for glutamine). 1-25 of these repeats can be classed as normal. Over 26 repeats begins to encroach on the disease's borderline, and those with above 40 repeats will invariably develop Huntington's disease. Huntington's disease occurs in adulthood, anywhere from mid-twenties onwards, generally. By observing the genetic sequence of a baby, it can be deduced not just whether they will develop Huntington's disease, but at what age they will begin to be affected by its symptoms. This is a triumph of gene sequencing and promises to give us insight into how hereditary diseases such as Huntington's can be treated.

Glutamine is also important in the regulation of ammonia levels in the body. Glutamine is very similar to glutamate, and features an additional amino group. This amino group (essentially ammonia) is ligated to glutamate, thus forming glutamine, by the enzyme glutamine synthase. The activity of this enzyme is tightly regulated and is important in ensuring that levels of ammonia do not rise to dangerous levels in the body.

Answer: Serotonin

The key feature of tryptophan (and serotonin) is its indole group - a double ringed structure that exhibits aromaticity. Serotonin is synthesised from tryptophan in a two-step process, firstly hydroxylation and then decarboxylation. Serotonin binds to a group of G-protein coupled receptors known as 5-HT receptors and they regulate food intake and mood, amongst other things. The protein that mediates the transport of tryptophan across cellular membranes also mediates the transport of the other aromatic amino acids (phenylalanine and tyrosine). An abundance of these competing amino acids may limit the intake of tryptophan and so may be linked to feelings of depression (a direct consequence of low levels of serotonin).

Tryptophan is an essential amino acid and so must be obtained from our diet. It is plentiful in sunflower seeds, bananas, and chocolate (hence the good stuff's association with happiness). Whilst we are unable to produce tryptophan, organisms such as E. coli can. The synthesis of this amino acid in E. coli is regulated by a group of enzymes coded for by genes which make up what is known as the Trp operon. The transcription of these genes (and therefore the level of tryptophan synthesis) is directly controlled by the amount of tryptophan in the cell, thus preventing overproduction.

Answer: Serine

Trypsin, chymotrypsin, thrombin, and acetylcholinesterase are all serine proteases, since they possess a serine residue at their active site which functions as a nucleophile (an electron pair donor). Serine proteases are actually defined by three residues at their active site - Ser195, Asp102, and His57 - which are collectively known as the catalytic triad. Working together, these three residues bring about the hydrolysis of peptide bonds, which otherwise links amino acids to one another in proteins.

The serine proteases hydrolyse peptide bonds via the same biochemical mechanism. However, each of the enzymes listed above has specific substrates. For example, trypsin cleaves the peptide bonds directly after positively charged amino acids (lysine and arginine), whereas chymotrypsin cleaves after bulky hydrophobic residues (phenylalanine, tryptophan, etc.). This specificity is determined by an amino acid binding pocket. This pocket in trypsin is long, narrow and contains a negatively charged carboxylate group at its end, making it a perfect fit for the side chain of either lysine or arginine.

Answer: Phosphorylation

Phosphorylation was known to occur at serine and threonine residues, and the discovery of phosphorylated tyrosine residues came later. The proteins listed in the question - epidermal growth factor receptors and insulin receptors - belong to the receptor tyrosine kinase family of proteins. They normally reside in the cell membrane and they bind to specific substrate molecules via their extracellular domains. Upon substrate binding, the receptor dimerizes and auto/trans-phosphorylation of tyrosine residues occurs. These phospho-tyrosines act as important docking sites for proteins which help to transmit the signal into the cell.

The dimerization of these receptors is an example of a transient protein-protein interaction (PPI). This is opposed to obligate PPIs (e.g. haemoglobin). Both types of PPI are interesting (yet daunting) prospects for drug-developers. PPIs are numerous and their dysfunction is linked to several human diseases. The development of drugs to specifically target these interactions is therefore an important goal, but one that is proving difficult. PPIs, unlike protein-substrate interactions, are large and fairly non-descript, making it tricky for small drug molecules to act specifically.

Answer: They are phosphorylated, which increases cell proliferation

Although phosphorylation of lysine has been observed in mammals, it is extremely rare and there exists no evidence that it induces cell proliferation.

Lysine and arginine are common in histones (the proteins which, with DNA, make up chromatin). The methylation of these residues regulates the expression of the genes that are proximal to the histone that is being modified.

Lysine residues are the targets of several types of post-translational modification. One of the best understood of these is ubiquitylation. The addition of ubiquitin to lysine residues can lead to the protein being recognised by the proteasome, which then proceeds to destroy the protein. Any other modification of lysine - whether it is methylation, acetylation, or SUMOylation - can be seen as competing with ubiquitin and so stabilises the protein. For more information on post-translational modification of proteins, please play my quiz "Putting on the Finishing Touches".

Answer: It is often removed during protein processing

The "start codon" is AUG and it is required for translation to begin. AUG codes for methionine and so this is the first residue in the polypeptide chain. However, after (and sometimes even during) translation, the protein is processed/modified, with bits being added and bits being chopped off - here, methionine is often lost.

Like cysteine, methionine is a sulphur-containing amino acid and so is especially prone to oxidation. Methionine often performs a stabilising role in proteins, and so its oxidation (by reactive oxygen species or other free radicals) can lead to protein damage and ageing.