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Segrapedia

Proteins

By Kevin She
2 Dec 2015

So what is a protein anyway? In the context of a meal, protein is often a piece of meat, typically muscle from an animal or fish. Other foodstuffs can also be high in protein, too. In the context of a cell, a protein is a macromolecule composed mainly of a chain of amino acids and each cell has a vast number of different proteins; there are approximately 20,000 to 25,000 genes that code for proteins in the human genome and many of these genes can make slightly different forms of the same protein (splice variants). Proteins make up the primary machinery that allows a cell to perform its functions.

In a cell, a protein is a single molecule made up of a long string of amino acids. Each amino acid has two ends and a tail (side chain) that hangs between the two ends. One of the ends is a nitrogen atom – the amino end or amino terminus , and the other end is a carbon atom – the carboxy end or carboxy terminus. Proteins start from the amino terminus of an amino acid; additional amino acids are added (polymerized) onto the carboxy terminus by joining the next amino acid’s amino terminus to the first amino acid’s carboxy terminus. In human and other eukaryotic cells, the average protein length is about 450 amino acids long but some proteins can be much longer, such as the giant Titin protein that can weigh in at between 27,000 to over 33,000 amino acids1. Some proteins are composed of multiple individual subunit proteins.

Remember that side chain hanging off the middle of an amino acid? Each amino acid has a different side chain and it is its shape and properties and the order in which they are strung together that will ultimately dictate the overall shape and function of the protein that they make up.

Figure 1 Lysine

Figure 1 Lysine: What’s Going On?

The figure on the left is the Fischer projection of the amino acid lysine made up of carbon, hydrogen, oxygen, and nitrogen atoms. The figure on the right is a space-filling model for lysine. The grey ball between the two red balls on the top right ball represents the carbon atom of the carboxy terminal and the blue ball to the left and slightly behind that is the nitrogen atom of the amino terminal. The blue ball on the bottom of the picture is the terminal nitrogen atom of the side chain.

In eukaryotes, which human cells belong, there are 21 common proteinogenic (makes proteins) amino acids. 9 of these are considered “essential” amino acids; they can only be obtained through dietary sources. These are phenylalanine, valine, threonine, methionine, leucine, isoleucine, lysine, and histidine. There are six amino acids that are considered conditionally essential; only in some situation, such as in premature infants or individuals with chronic amino acid deficiency, are dietary sources of these amino acids required. These six are arginine, cysteine, glycine, gluatmine, proline, and tyrosine. The remaining dispensable amino acids are alanine, aspartic acid, asparagine, glutamic acid, and serine. Alanine, for example, can be manufactured by our cells from valine, leucine, or isoleucine. Aspartic acid and asparagine, on the other hand, are generated as a byproduct of by our cells’ metabolism and glutamate. Likewise, glutamine and serine is also made from metabolic byproducts in eukaryotic cells.

Severe amino acid deficiency leads to kwashiorkor, a common disease in regions of pronounced food insecurity. Mild amino acid deficiency can result in more subtle symptoms such as poor immune response, chronic fatigue, slow recovery from injuries and exercise, and swelling of the hands, feet, or abdomen. A varied diet, even a vegetarian or vegan one, is the most simple way to avoid amino acid deficiency. Conversely, very high protein diets pose potential risks for significant harm in individuals with chronic kidney disease2. However in healthy individuals, high protein diets are relatively benign although these diets are associated with increased risk of developing kidney stones.

There are other amino acids, such as GABA, that are typically not incorporated into proteins. GABA, in particular, serves as a neurotransmitter in the central nervous system. Likewise, D-serine (right-handed, or D-stereoisomer, serine) acts as a co-activating neurotransmitter in the brain. Normal proteinogenic L-serine and is converted into the non-proteinogenic right-handed form by enzymes in the brain. Most eukaryotic proteinogenic amino acids are L-stereoisomer (levorotatory; a pure solution of a levorotatory molecule rotates plane polarized light counterclockwise, or to the left; a pure solution of a dextrorotatory molecule rotates plane polarized light clockwise, or the the right). A number of other amino acids are also converted into neurotransmitters such as tryptophan (precursor for serotonin), tyrosine (precursor for dopamine, epinephrine, and norepinephrin), and arginine (precursor for nitric oxide).

The first amino acid that was discovered was purified from asparagus juice in 1806 and was named asparagine. Asparagine has a relatively simple side chain consisting a chain of two carbon atoms ending with an oxygen and a nitrogen atom, in contrast with lysine’s long floppy side chain. It is primarily the length and composition of the side chain that gives amino acids both their general and their specific functions.

In the cell, proteins are made in ribosomes: messenger RNA, the recipe for a protein, is threaded through a ribosome and specific amino acids are strung together in the order that the messenger RNA dictates. The newly synthesized protein is progressively extruded from the ribosome as additional amino acids are added to it. As it exits the ribosome, the side chains interact with the water molecules, salts, and parts of itself that had previously been extruded. Based on the nature and order of the amino acid string being extruded, the linear protein begins to fold in on itself into a three dimensional structure.

This three dimensional structure is what gives proteins the properties that they possess so they can fulfill their function in keeping a cell in operation. Many proteins must even combine with other proteins (subunits) in order to create a functional multi-subunit protein. Proteins serve many different functions within a cell. For example, actin are strings or filaments of individual actin proteins that crisscrosses throughout every cell and helps determine the shape of the cell and act as highways for moving vesicles (small sacs made up of lipids) that move material around to different parts of the cell. In “Art of the Cell” (YouTube) by John Liebler; starting at about 1:15 into the video, is a fantastic animation of a myosin motor dragging a vesicle along an actin filament.
Link: What’s Going On?

The video starting around 1:15 depicts a myosin motor protein attached to a vesicle (the large sac) and an actin filament (composed of many actin molecules strung together). The myosin motor “walks” down the actin filament by transferring energy from ATP (adenosine triphosphate) molecules to change its own shape. Each ‘step’ uses energy from an ATP molecule.

The little studs sticking out of the vesicle are proteins; these can serve various functions. Vesicles have proteins studded on their outside that serve as a “delivery address,” other proteins may serve as a “contents label,” and if a vesicle is for transporting proteins to the surface of the cell, the intracellular parts of these surface proteins will stick out of transport vesicles.

What is not clearly shown, in the interest of clarity, are ubiquitous water molecules and salt ions that permeate all of the open spaces. Also, the density of proteins in a cell is typically much higher.

Figure 2 Vesicle

Figure 2 Vesicle: What’s Going On?

For a sense of scale, the vesicle featured in “Art of the Cell” is roughly of a similar size to a synaptic vesicle; a vesicle that holds neurotransmitter to be released into a synaptic cleft between two neurons in the brain.
From left to right:

– drawing of half (sagittal section) of a human brain; the human brain is about 1200 mL (1.2 quarts) and about 1.5 kg (3.3 lb). There are about 100 billion neurons and upwards of a trillion glial cells in a typical brain. Fun fact; part of Albert Einstein’s brain had a much higher glia to neuron ratio than the average person3.

– drawing by Ramon y Cajal of the hippocampus after Golgi staining. To this day, it is unknown why only a very few neurons are stained using that method, but it allowed the first visualization of individual neurons within the brain. An average human hippocampus is approximately 7 cm (2.75 inches) long and 2 cm ( 0.75 inches) wide.

– scanning transmission electron micrograph (picture) of a synaptic junction, the point of interface between two neurons. There are approximately 150 trillion synapses in the human brain. That is about 500 times the number of stars in the milky way galaxy. The bottom left is a tiny part of a “post-synaptic” neuron with receptors to detect neurotransmitters released into the synaptic cleft. The middle portion shows a tiny part of a “pre-synaptic” neuron with reserves of neurotransmitter-containing synaptic vesicles waiting to dock at the terminal and release neurotransmitter into the cleft. The entire width of the picture is approximately 2 μm (micrometer), about 1/50th of the width of a human hair.

– space-filling model of a synaptic vesicle by Takamori et al 2006 (Cell)4 and the proteins that can be located on the outside surface of a synaptic vesicle. The average diameter of a vesicle is approximately 40 nm (nanometer). 2,500 vesicles placed end to end are about the width of a human hair.

Proteins fulfill many diverse functions within a living cell. Like actin, there are many proteins that fulfill structural roles such as histones that determine which parts of the genome are accessible for transcription. In other words, it acts as a gatekeeper or librarian who makes sure that only the genes that particular cell type requires is available to be made. Other structural proteins include the PSD-95 family of proteins that form scaffolds that determine what kinds of receptors and how many of them are allowed to reside in each specific synapse in each neuron. Yet other structural proteins reside on the cell surface and adheres that cell to other cells in a very specific manner. Interestingly, a specific subgroup of this class of extracellular adhesion protein in neurons can specify what kind- and where- a new synapse will be formed.

Muscles are very rich in actin and myosin; these proteins are arranged in repeating units and mediate muscle contractions as they crawl along one another. The very high density of these two proteins contributes to the high protein content of dietary meat. Although plants don’t have muscles, plant cells still contain protein, albeit less than in animal muscle cells. Additionally, different plants have different abundances of different amino acids and is typically different than the abundances of different amino acids in animal cells.

Almost all metabolic processes in a cell rely on enzymes. Enzymes accelerate, or catalyze, complex chemical reactions and allows them to occur at pressures, temperatures, and speed necessary for life. Enzymes are typically proteins although aptamers made from RNA molecules can also have catalytic effects. Enzymes work based on their shape; they can bring two different molecules together so they can join or change the shape of a molecule so it can be broken into smaller pieces. Some enzymatic processes occur based solely on shape but many enzymes use energy, typically ATP, in order to mediate a chemical reaction. ATP is the abbreviation for adenosine triphosphate, a nucleic acid with three phosphates attached to it linearly. Enzymes can cleave off the phosphates to release the potential energy and uses that energy change the shape of the enzyme or to transfer that energy to itself or another protein.

For example salivary amylase, a protein enzyme secreted with saliva, catalyzes the breakdown of starches into simple sugar. When you chew a plain saltine cracker, it initially has little taste. However, as you continue to chew the cracker it can start tasting a little bit sweet. It is the salivary amylase progressively breaking down the starches into simple sugars.

There are tens of thousands of different discrete chemical reactions that must occur in a very highly controlled manner to support the function of a cell. Many of these reactions occur in a step-wise manner and each step may require a separate enzyme. The metabolic pathways required for the proper function of a cell is beautifully complex (Roche).

Another important role that proteins play is in signal transduction. Signal transduction, also known as cell signaling, is the transmission of signals from one part of the cell to another. The transmission of signals from the exterior of the cell to its interior is a major route for signal transduction. The signal is typically passed on from one protein to another via mechanisms very similar to how enzymes catalyze chemical reactions. Many signal transduction events require energy in the form of ATP or other molecules to change the shape of the downstream (next) protein down the line.

Signals from outside of the cell are detected by cell surface receptors; specialized proteins that can detect the presence of something, resulting in a change of the shape of the receptor (receptor conformation), and relay that change to downstream signaling proteins. There are also receptors inside of the cell (intracellular) that can detect the presence or abundance of particular molecules. For example, there are receptors on the surface of neurons in the brain that detect the presence of neurotransmitters and then relays that signal to the inside of the cell. Other receptors, such as taste receptors on cells on the tongue, detect the presence of specific molecules. For example, a sugar molecule freed from starch by salivary amylase “fits” into a pocket of receptors that detects sugar. This causes a change in the shape of the receptor and the signal is relayed to inside of the cell. Yet other receptors such as the Toll-like receptors, that are present in a wide range of cells but are most prominent in immune cells, can detect “pathogen associated molecular patterns” (PAMPs) that are shed by microorganisms that can be harmful or pathogenic to humans. Upon detection of these microbial molecules the receptor signals for an immune response.

Many of these signals, like passing a relay baton from one runner to another, eventually ends up in the nucleus of a cell. The nucleus is where the genome is stored in the form of coiled up DNA, and is the source of all instructions that a cell can perform. In addition to structural proteins that determine which parts of the genome are accessible, other proteins called transcription factors can be activated through signal transduction to bind to very specific parts of the genome. Depending on the transcription factor and the gene in question, the transcription factor can either promote or prevent the expression of that gene or dictate which version of that gene will be made.

Finally, another major class of proteins are pores and pumps. The main feature of this class of proteins are that they can form a channel within the central part of the protein and that they span membranes; either the outer membrane of the cell or interior membrane compartments within the cell including the nuclear membrane, the endoplasmic reticulum, the golgi apparatus, the membranes of mitochondria, and others including all of the various –somes (lysosome, endosome, etc.) and vesicles.

Most pore proteins can typically be opened or closed by changing shape much like enzymes. Many pores, especially in the central nervous system, are also receptors that open and close depending on the presence or absence of neurotransmitters, allowing or preventing ions from crossing into or out of a cell. This flow of ions follows osmotic pressure gradients, which must be maintained by pump proteins that use energy, also typically in the form of ATP, to change shape and force ions through cell membranes across the osmotic gradient (pushing ions “uphill”). Although of utmost importance in neurons of the central nervous system, all cells have pumps to maintain the proper ion concentrations inside the cell.


References

1. Wang, K., McClure, J., & Tu, A. Titin: major myofibrillar components of striated muscle. Proc. Natl. Acad. Sci. U.S.A. 1979; 76(8): 3698-702

2. Friedman, AN. High-protein diets: potential effect on the kidney in renal health and disease. Am. J. Kidney Dis. 2004; 44(6): 950-62

3. Diamond, MC, Scheibel, AB., Murphy, GM. Jr., & Harvey, T. On the brain of a scientist: Albert Einstein. Exp. Neurol. 1985; 88(1): 198-204

4. Takamori, S., Holt, M., Stenius, K., Lemke, EA., Gronborg, M., Riedel, D., Urlaub, H., Schenck, S., Brugger, B., Ringler, P., Muller, SA>, Rammer, B., Grater, F., Hub, JS., De Groot, BL., Mieskes, G., Moriyama, Y., Klingauf, J., Grubmuller, H., Heuser, J., Wieldand, F., & Jahn, R. Molecular anatomy of a trafficking organelle. Cell. 2006; 127(4): 831-46