Unraveling Reality {18}

Proteins

“To a large extent, the structure, behavior, and unique qualities of each living being are a consequence of the proteins they contain.” ~ American molecular biologists Kathleen Park Talaro & Barry Chess

Cells and their components are the handiwork of proteins. A protein is a large, complex, organic (carbon-based) molecule; a macromolecule manufactured in an intracellular factory called a ribosome.

Ribosomes

“The ribosome is universal biology.” ~ American biochemist Loren Williams

Ribosomes are composed of 55 to 80 proteins, depending on organism type. With a precise architecture and composition, the structural proteins within ribosomes are unusually short, and uniform in length. Also situated within a ribosome are 2–3 strands of RNA, which ostensibly provide the instructions for making proteins. The RNA accounts for up to 70% of the total mass of a ribosome.

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For a cell to divide into 2, it must have at least 2 functional ribosomes, so that each daughter cell can make the proteins it needs. Hence, the speed at which ribosomes can reproduce themselves limits how fast cell division can occur.

“Think of ribosomes not as a group of carpenters who merely build a lot of houses, but as carpenters who also build other carpenters. There is an incentive to divide the job into many small pieces that can be done in parallel, to more quickly assemble another complete carpenter to help in the process.” ~ Swedish systems biologist Johan Paulsson

Self-replication of the smallest and fastest ribosome takes at least 6 minutes; most take more time. This is the temporal boundary that limits bacterial growth.

Ribosomes are constructed for optimal self-production efficiency, both by the number of proteins and their composition. Ideally, ribosomal proteins should be ~3 times smaller than an average cellular protein, and they should all be roughly similar in size – just as they are.

Because cells can make ribosomal RNA much faster than proteins, the more RNA that a ribosome has, the more rapidly a ribosome may be produced. Hence, ribosomes are stuffed with as much RNA as possible, to maximize the rate at which more ribosomes may be made.

“Any place the ribosome can get away with using RNA, it should use it, because self-production speed can essentially be doubled or tripled. Even if RNA were inferior compared to protein for enzymatic function, there is still a great advantage to using RNA if a cell is trying to produce ribosomes as fast as possible.” ~ Johan Paulsson

Such heavy use of RNA holds mostly for self-producing ribosomes. Most other cell structures do not self-produce and can therefore sacrifice production speed for the quality control provided by using proteins instead of RNA.

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While many ribosomes churn out a wide variety of proteins, some specialize to manufacture only certain products. A single cell may have thousands of tailored ribosomes.

The protein production process is intricate. To ensure proper-functioning products, ribosomal machinery is itself subject to quality control.

Because ribosome assembly is so energy costly and only desired when cells are growing, ribosome assembly is highly regulated in response to available nutrients and external stimuli.

“A quality control function exists that uses the system to do a test run. If ribosomal subunits don’t pass, there are mechanisms to discard them. It’s the most elegant and efficient way to produce perfect ribosomes.” ~ American molecular biologist Katrin Karbstein

The basic recipes that ribosomes use to produce proteins are termed genes. The actual manufacture of proteins often involves appended notes not found in genes. These are epigenetic modifications, which are expressed chemically in a variety of ways. The prefix epi is Greek for “outside of.”

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Proteins are a cell’s population of workers, who not only maintain the cell, but also create its successor.

“Proteins are responsible for nearly all cellular processes. The cell has to make a huge variety of proteins and target them to the precise location where they are needed to function.” ~ English biochemist Vicki Gold

Once off the production line, proteins preen themselves by folding into a globe or fiber. This posturing is a product of energetic economy.

The elite, most energetic proteins are enzymes. Enzymes distinguish themselves by their hyperactivity, in being able to catalyze and regulate biological reactions.

Within a cell there are around 3 million proteins per cubic micron (µm), which is the smallest prokaryotic cell size. Prokaryotes are ~1–5 µm in size; eukaryotes ~10–100 µm. Proteins comprise a prodigious cellular workforce. A single yeast cell has 42 million proteins.

“The self-association of proteins into symmetric complexes is ubiquitous in all kingdoms of life. Proteins evolve on the edge of supramolecular self-assembly.” ~ molecular biologist Héctor García-Seisdedos et al

The various structural facets of a protein – chemistry, shape, fold pattern, and assembly – are all significant in its functioning. A protein at work – chemically communicating, physically morphing, actively manipulating – is an incredible sight.

“The biological properties of a protein depend on its interaction with other molecules.” ~ English cytologist John Wilson

Most proteins are multifunctional; but they often need to be focused to a specific task, else they might create cellular havoc, creating disease. This is not to say that proteins are mindless molecules. Quite the contrary.

For example, a single protein controls when to start plant flowering. Without the savvy self-control of this protein, plants flower too early.

Besides knowing what to do, proteins know exactly what they are doing, and so are prepared for what needs to be done next. For example, by binding to an ion, a protein activates its work toolkit. The state of a protein at any instant embodies a memory of its past.

DNA-binding proteins regulate the activities of various genes, so that cells carry out the correct tasks at the right time. For this to work, these proteins need to promptly find the precise DNA site.

“That there are many obstacles in the way when proteins are to diffuse along DNA strands.” ~ Swedish molecular biologist Johan Elf

Despite the obstacles and needing to look through literally millions of selfsame binding alternatives, proteins make their way to the right DNA site within a very few minutes.

Unsurprisingly, the massive armies of working proteins in a cell must be supervised to properly play their roles. There are various physical mechanisms to achieve this necessary governance. What can never be seen under a microscope is the active knowledge needed to manage a cell, especially the vast workforce of proteins within. Physically, a cell’s life is an ongoing miracle, as the intelligent forces behind biomechanics remain enigmatic.

The human body synthesizes ~100,000 different proteins. For cells (and bodies) to function, specific proteins must be produced in appropriate numbers in a timely manner. That takes large-scale communication and coordination; whence forth such cognitive skill to manage such complex production quotas and schedules?

Once minted, neophyte protein laborers must head off to work, doing a proper job at the right location. Though tasks may be completed, the work of proteins is never done – cellular construction and maintenance are ceaseless.

 Prison-Keeping Proteins

Proteins in cells keep an eye out for miscreants. The vaccinia virus is a poxvirus, related to smallpox. When a vaccinia makes its way to a cell membrane to launch itself toward another cell and further infect a multicellular host, a septin may spot it.

Septins are a diverse family of cell-membrane proteins which selectively form groups to help manage various cell processes. Septins decide their grouping depending upon what needs to be done.

“Septins play important roles in many fundamental cellular processes, including division, migration, and membrane trafficking.” ~ Austrian cytologist Julia Pfanzelte

A septin snags a vaccinia and makes itself into a cage so that the virus is caught and can commit no more malice.

“Septins exert their antiviral effect by forming cage-like structures around viral particles to suppress release from infected cells.” ~ English cell biologist Michael Way

Septins have also been seen incarcerating bacterial pathogens.

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“Amino acids adjust to the requirements of the rest of the protein.” ~ English molecular biochemist Richard Goldstein

Proteins evolve based upon the amino acids needed for specific tasks, albeit within the physicochemical constraints imposed by proteins being able to enfold into an energy-economical shape when taking a break. A protein consumes no energy when curled in repose. A protein’s shape is entirely determined by its unique amino acid sequence. So, the amino acids in a protein are selected based upon information content, functional import, and biomechanical properties.

The proximate causes of a protein’s specificity are its biophysical properties; the ultimate causes are the evolutionary processes that brought those biophysical mechanisms into being. ~ American evolutionary biochemist Michael Harms

The amino acids in proteins must fit an atomically specific spatial configuration with an exact energy signature. Given the intricacy involved, the evolution of proteins cannot be accounted for solely through biochemistry, nor even explained via physical genetic coding. An intelligent force of coherence must be involved.

 Hormone Evolution

“New molecular functions can evolve by sudden large leaps due to a few tiny changes in the genetic code.” ~ American evolutionary biologist Joe Thornton

Hormones are signaling molecules. They are produced in endocrine glands and transported in the circulatory system.

Hormones work because proteins pay attention to them. A hormone with no protein receptor has no reason to be.

The earliest steroid hormone receptor recognized only estrogens, which are the primary female sex hormone. Estrogens also play important physiological roles in males too.

Changes in just 2 letters of the genetic code in our deep evolutionary past caused a massive shift in the function of 1 protein and set in motion the evolution of our present-day hormonal and reproductive systems. ~ Joe Thornton

500 million years ago an editing of just 2 amino acids in the estrogen hormone receptor invoked a ~70,000-fold change in the protein’s specificity, allowing the protein to tune in on other steroid hormones. This minor tweak to enliven hormone receptivity afforded a revolution in how multicellular organisms develop and reproduce.

” If those 2 mutations had not happened, our bodies today would have to use different mechanisms to regulate pregnancy, libido, the response to stress, kidney function, inflammation, and the development of male and female characteristics at puberty.” ~ Joe Thorton

The change of 2 amino acids in the receptor protein was a pre-adaptation: an adaptation that is employed in later evolution. In this instance, it was an incredibly efficient genic editing that permitted much grander sophistication in physiological functioning.

“Scores or hundreds of amino acids participate in a dense network of interactions to determine protein structure, dynamics, and function.” ~ Michael Harms et al

Considering the complexity of proteins, the precise modesty of the modification in the hormone receptor and its outsized impact suggests a forward-looking savvy at work in crafting evolution.