The Life of a Protein in Ten Questions Quiz

Answer: Ribosomes

As mentioned in the question, all the proteins in our cells (and there are many - diverse as they are numerous) arise essentially from four nucleotides - A, C, G, and T - in DNA. These stretches of DNA (known as genes) code for mRNA (the "m" standing for messenger, as these molecules carry a message from the nucleus to the cytoplasm), which again are made up of just four different nucleotides - A, C, G, and U. How these nucleotides code for amino acids was a point of contention between scientists for many years, with Francis Crick (co-discoverer of the structure of DNA) arguing for a complex and overlapping two-nucleotide system. The truth is much simpler. The four nucleotides can combine to form various three-letter arrangements (sixty-four, to be exact) known as codons. One codon codes for a "start" codon, three codons for a "stop" codon, and the remaining codons for the other amino acids. The more eagle-eyed quizzer will see that the numbers don't quite add up (sixty codons, but only twenty amino acids?). In fact, the "start" codon codes for the amino acid methionine. The remaining nineteen amino acids share the fifty-nine remaining codons, with some amino acids being coded for by more than one codon (arginine alone is coded for by six codons!).

The ribosome is an interesting beast. It is a small but complex machine of the cell which firstly recognises the mRNA codons, and then recruits molecules known as tRNA (the "t" here stands for transfer) which deliver the appropriate amino acids. It consists of a "large" subunit and a "small" subunit, which work together poetically to create proteins from mRNA codes - a process known as translation. Ribosomes are a mixture of proteins and nucleic acids, and it came as somewhat of a shock to the scientific community to realise that it was the nucleic acid (and not the protein) which carries out the catalytic activities of the ribosome. This finding, deduced from detailed structural analysis of ribosomes, earned Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath the 2009 Nobel Prize for Chemistry.

Answer: The peptide bond

In the builder analogy, the peptide bond would be the cement. Amino acids are very aptly and cleverly named, as they contain both an amino group and a carboxyl (acidic) group. The amino group from one amino acid and the carboxyl group from another undergo a reaction and become covalently linked, meaning that they share electrons. This reaction is called a condensation reaction, as water is released upon the formation of the peptide bond (the H20 is formed by one H+ ion donated by the amino group and one OH- ion donated by the carboxyl group). In chemistry, we are told that bonds can be single (which are capable of rotation) or double (which cannot rotate)*. The peptide bond is somewhere in between these two classifications, and as such has restricted rotation.

*There are other types of bond, but these are not relevant here and so will not be discussed.

Answer: The alpha helix

Shortly after a protein is synthesised, alpha helices are often the first discernible structures to form. Along with beta sheets, alpha helices make up what is known as a protein's secondary structure. The secondary structural elements can then combine in various ways to form the protein's tertiary structure, which determines the protein's function.

The alpha helix was first proposed by Linus Pauling (the undisputed king of structural biology) after studying their x-ray diffraction patterns. Alpha helices form quickly and spontaneously following protein synthesis (translation) in an attempt to reduce the number of unpaired hydrogen bond donors and acceptors*. By looking at a protein's primary structure (another term for the sequence of amino acids), one can deduce some aspects of the protein's structure. For example, some amino acids are more likely to form alpha helices than others. Additionally, a stretch of around twenty-six hydrophobic amino acids suggests that the protein is membrane-bound. Interestingly, the amino acids which are least likely to be found in alpha helices in normal circumstances (namely glycine and proline) are far more likely to be found in alpha helices in membrane-bound proteins, since they offer a greater ability to change the protein's conformation.

*Each peptide bond contains hydrogen bond donors and hydrogen bond acceptors which can form hydrogen bonds with donors/acceptors with nearby amino acids. It is one theory ("theory" in the non-scientific sense in that it is not supported by sufficient evidence so as to be generally accepted) that a hydrogen bond between a peptide bond and another peptide bond is more stable than the hydrogen bond between a peptide bond and a water molecule, thus making the hydrogen bonds in structures such as alpha helices energetically favourable.

Answer: Chaperones

Chaperones assist the folding of de novo proteins. They also assist the unfolding of misfolded proteins. Finally, they can assist the transport of proteins across membranes. Chaperones exist as several families of proteins. One such family are the chaperonins (or Hsp60 proteins). These are cage-like structures which assist the folding of proteins in an ATP-dependent manner. One of the best characterised of this family is the GroEL/ES protein in bacteria.

A second major group of chaperones is the Hsp70 proteins, which have diverse targets and which (again) utilise ATP in the folding process. Though Hsp70 is an ATPase (i.e. it is innately capable of hydrolysing ATP), this activity is low and so is usually induced by another protein called Hsp40.

The folding process of proteins is interesting and controversial in the field of biology. For more information on this topic, please play my quiz "Solving Levinthal's Paradox".

Answer: False

Proteins are far from rigid. Although their shape determines their function, functionality is often dependent on a variety of conformations and the efficiency of a protein in carrying out its function is often determined by its ability to shift between these conformations. Perhaps the best example to reflect my point is enzymes. Enzymes are one of the most miraculous things in nature, and can carry out biochemical reactions that are (and almost certainly will always be) out of the realms of possibility for man-made catalysts when it comes to efficiency.

The chemistry of enzyme-based reactions occurs at the active site of the enzyme. It was originally thought that the active site of an enzyme was the exact fit for its target substrate, and the perfection with which the two slotted together explained enzyme efficiency.

This is called the Lock and Key hypothesis and was suggested by the biochemist Emil Fischer. With increased understanding of enzyme dynamics and advances in structural biology, it became apparent that this hypothesis was unsuitable. By studying the crystal structure of a protein called lysozyme, it was found that its active site was most complimentary to the shape of the substrate only when the protein-substrate complex was formed.

This led to the Induced Fit hypothesis, as proposed by Daniel Koshland. Generally, crystal structures have supported the Induced Fit hypothesis. Other theories have since been put forward, one of which in particular shows promise in rivalling the Induced Fit hypothesis for catalysis, though this will be discussed in another quiz.

Answer: Cooperativity

Haemoglobin exists not as one conformation, but as several conformations which are constantly changing, and which are in a state of thermal equilibrium. One of the many conformations is the "correct" one and the one most likely to bind to oxygen. Upon binding oxygen, there is an equilibrium shift so that more of the haemoglobin molecules adopt this "correct" conformation. The conformational change coupled to this is transmitted to the other polypeptides of haemoglobin, which themselves change conformation and become more likely to bind oxygen. This is described by the Monod-Whyman-Changeaux model.

The ability of haemoglobin to bind substrate cooperatively contrasts with myoglobin. Whereas myoglobin has only one binding site and so binding is all or nothing, haemoglobin introduces a degree of regulation in its binding by allowing its four polypeptides to communicate to one another as to whether or not they have bound to oxygen. This system allows the amount of oxygen bound by haemoglobin to be in proportion to the partial pressure of oxygen in the environment.

Answer: Fibrous

We are taught that proteins can be globular or fibrous. Globular proteins are generally smaller and more compact, and are soluble in water. Examples of globular proteins include haemoglobin, most enzymes, and signal proteins. Fibrous proteins tend to be larger, longer, and insoluble in water. A common feature of fibrous proteins is cross-linking between protein filaments (such as the case with collagen) which gives high tensile strength. As mentioned already in this quiz, proteins are team players and often regulate their own function by interacting with other proteins. The best example to demonstrate this is actin. Actin exists as monomers in the cell cytoplasm (known as G-actin, with "G" standing for globular, since they are compact and soluble) and can interact with other actin monomers to form F-actin ("F" standing for fibrous) which makes up the insoluble cytoskeleton.

Alongside globular and fibrous, a third classification of protein exists. These are the membrane proteins. For more information on membrane proteins, please play my quiz "Never Work With Membrane Proteins".

Answer: PEST sequences

Proline (P), glutamate (E), serine (S), and threonine (T) are enriched in PEST sequences. Advances in amino acid-sequencing techniques showed that proteins that were known to have short half-lives (such as p53, known as the "guardian of the genome") were enriched in these four amino acids. Database searches to find other proteins that also contain PEST sequences supported the link with a short lifespan.

It seems likely that PEST sequences shorten the lifespan of proteins by being inherently unstable. Proteins rich in PEST sequences are therefore more likely to become denatured and subsequently bound by protein-destruction machinery.

It is also thought by some that PEST sequences may act as signals to specifically recruit proteins involved in their destruction.

Answer: Plaques

In cells, proteins fold into their native (correct) shape almost seamlessly (again, my quiz "Solving Levinthal's Paradox" provides greater detail on this topic), but some proteins may misfold. Unfolded or misfolded proteins can be bound either by chaperones, which attempt to fold/refold the protein, or by proteins which mediate its destruction. The longer a protein remains unfolded/misfolded, the more likely it is to bind this latter group of proteins and so be destroyed. While this may sound like a bad thing, it is actually beneficial to the cell, as misfolded proteins possess exposed hydrophobic patches which can lead to aggregation and the formation of amyloid plaques, leading to diseases such as Alzheimer's disease.

"Classical" plaques exhibit a high amount of beta sheet secondary structure. It is believed by some (though not by all) that plaques form because beta sheets are the most stable structures that a protein can form and so there is a constant struggle for the protein to maintain its native structure, rather than the more stable (yet inactive) beta sheet-rich form. The implication here is that the native structure of a protein is not its most stable conformation (which has been a leading theory on what drives protein folding).

Answer: They are recycled to make new proteins or are converted into different biomolecules

The process of protein synthesis and degradation is referred to as protein turnover, and a balanced protein turnover is essential to maintain healthy cells. The proteasome generally breaks proteins down into fragments of around six amino acids, which can then be degraded further by other cellular enzymes to yield individual amino acids which are then used to synthesise new proteins. Amino acids can be synthesised from other biomolecules in the body, but some (known as the essential amino acids) must be obtained from our diet. These essential amino acids include histidine, lysine, and tryptophan.

Amino acids can also be used to synthesise metabolic intermediates of the citric acid cycle, thus providing cellular energy when blood glucose is low. For example, aspartate (an amino acid) can be converted to oxaloacetate (a citric acid cycle intermediate). This is called an anaplerotic reaction .