Saturday, December 04, 2010


Molecules called proteins perform most of the functions of the cells of which all living things are composed.

Proteins are polymers, molecules synthesized by the chemical bonding together or polymerization of many other molecules called their monomers, and furthermore are copolymers, polymers composed of monomers of more than one kind, the monomers of the proteins being called amino acids, of which there are twenty different kinds.

And protein amino acid order determines protein function.


Molecules Called Proteins Perform Most Cell Functions

Living organisms are composed of cells, and most cell structures are formed or synthesized and most other cell functions performed by molecules called proteins.

Each such function is performed by its own particular and specific protein, or set thereof, and usually many molecules of each.

And a body cell typically synthesizes and uses tens of thousands of different proteins.


Proteins Are Copolymers

Proteins are polymers, molecules synthesized by the chemical bonding together or polymerization of many other molecules called their monomers.

Furthermore, proteins are copolymers, polymers composed of monomers of more than one kind.


Proteins Are Synthesized From Monomers Called Amino Acids

Proteins are synthesized from monomers called amino acids, of which there are twenty different kinds.

The amino acids are small molecules, composed of only ten to twenty-seven atoms each, depending on kind, averaging about twenty, and averaging in mass about 2.35 * 10-22 gram, about one-quarter of one zeptogram (sextillionth of a gram), or 235 yoctograms (septillionths of a gram), about eight times as much as the three-atom water molecule, an oxygen atom single-bonded to each of two hydrogen atoms (an oxygen atom forms two single bonds or one double bond in a molecule, while a hydrogen atom forms one single), the total mass of which is about 2.99 * 10-23 gram, or thirty yoctograms.

Every amino acid molecule consists of a central carbon atom single-bonded to a hydrogen atom, an amino group, a carboxylic acid group and a prosthetic group (a carbon atom forms four single bonds in a molecule, or one double bond and two singles, or two double bonds, or one triple bond and one single).

An amino group is composed of a nitrogen atom (which forms three single bonds, or one double and one single, or one triple) single-bonded to each of two hydrogen atoms.

And a carboxylic acid group is composed of a carbonyl group or moiety, a carbon double-bonded to an oxygen atom, further single-bonded to a hydroxy or alcohol group, an oxygen atom single-bonded to a hydrogen atom.

Such bonds and groups are of course the ordinary molecular bonds and functional groups of carbon chemistry, called "organic chemistry" due to life's taking such advantage of the ability of carbon to form large and stable molecules that all carbon on the face of the earth is or has been part of a living organism.

And the amino acid amino and carboxylic acid groups are of course what gives it its name.

Every amino acid is identical to every other in the above, regardless of kind, in a nine-atom moiety called here its invariant moiety, composed of its central carbon atom and the hydrogen atom and amino and carboxylic acid groups bonded to it.

And an amino acid of one kind differs from one of another solely in the elemental composition (the kinds and number of atoms involved), structure (how those atoms are bonded together) and consequent properties of its prosthetic group.


Amino Acids Are Chiral

A carbon atom bonded to four different atoms, groups or moieties is asymmetric, and forms an asymmetric center, and a molecule with a single such center can exist in one of two mirror-image forms or stereoisomers.

The stereoisomers in such case are distinguished by a convention based on chirality or handedness, the lowest-weight substituent being taken as the "thumb", the asymmetric carbon atom as the "palm" and the other substituents viewed along the "thumb-to-palm" axis and direction, and the "fingers" taken to curl in the direction of decreasing weight of substituent, with the "fingers" of the left-handed or levo (Latin for “left”) stereoisomer curling in a clockwise fashion, and those of the right-handed or dextro stereoisomer counter-clockwise.

A molecule with N asymmetic centers can exist in any one of 2N stereoisomeric forms.

And except in the simplest amino acid glycine, the prosthetic group of which is a single hydrogen atom, the amino acid central carbons each form an asymmetric center, and the amino acids can exist as either of the two possible stereoisomers, but are always found to be the levo stereoisomer in nature.


Proteins Are Polyamides

The amino acid amino and carboxylic acid groups are its bonding groups, which take part in the amino acid polymerization needed for protein synthesis, forming the necessary bonds between that amino acid and its neighbors in the protein.

Each such bond involves one of each kind of bonding group, with a loss of two small moieties amounting to the loss of a water molecule for every amino acid added to the protein, an amino group hydrogen and the carboxylic acid group's hydroxy group, amino acid polymerization being therefore what is called a dehydration reaction.

And the remaining amino and carbonyl moieties are single-bonded to one another, forming a connecting amide moiety (a carbonyl single-bonded to an amino moiety), the carbon-nitrogen bond of that moiety being the actual protein bond.

Proteins are therefore polyamide polymers or polyamides, as are the common artificial copolymers called nylon, although the resemblance should not be stretched too far.


Proteins Have Backbones And Side-Groups

The invariant moieties of the amino acids incorporated into a protein, minus water of polymerization, comprise what is called its backbone, an elongated and repetitive structure in which each invariant moiety remnant incorporated forms a unit identical to every other (although of course the end-units each bear a free bonding group unused in polymerization).

And the prosthetic groups of those amino acids become protein side-groups projecting from those protein backbone units and that backbone.


Proteins Are Oriented

Each protein backbone unit has one bonding group moiety on one side of its central carbon and the other on the other, in the same order for all backbone units in and along the protein backbone.

And each protein bond likewise has one bonding group moiety on one side of the protein carbon-nitrogen bond and the other on the other, in reverse order to that of the backbone units.

Such protein order or orientation or direction is referred to in terms of the free bonding groups at either end of the protein, with the direction from the free amino to the free carboxylic acid group being referred to as the "N-to-C" direction, and the opposite as "C-to-N".


A Typical Average Natural Protein
Length, Size, Mass And Gram Number

Proteins of different kinds and functions vary widely in the number of amino acids of which they are composed.

But three hundred amino acids is a typical natural protein length and size.

And a typical average natural protein mass can be calculated based on that length and size by multiplying the average mass of an amino acid (see section d above) times three hundred, and then subtracting the combined masses of the two hundred and ninety-nine water molecule equivalents lost (see section f), amounting to about 6.16 * 10-20 gram, about sixty zeptograms, a little over two thousand times the mass of a water molecule.

And the corresponding typical average natural protein gram number, the number of such proteins contained in one gram thereof, can be calculated by dividing that mass into one gram, giving about 1.62 * 1019 or about sixteen quintillion such proteins per gram.


Protein Amino Acid Order Determines Protein Conformation

Proteins can rotate around their backbone single bonds, and therefore all along their backbones, and consequently twist and coil, but the proteins which perform the functions of the cell generally assume three-dimensional coiled structures or conformations specific to their kinds, stabilized in various ways.

For example, attractions between positively- and negatively-charged moieties of molecules form what are called hydrogen bonds, which separately are weaker but collectively can be much stronger than any one molecular bond.

Such bonds between nearby backbone units along the protein backbone cause the assumption of winding or helical conformations along the backbone, as well as sheet conformations involving multiple turns and side-by-side runs thereof. Such interactions and resulting conformations are not specific to any particular protein or moiety thereof, since every backbone unit is identical to and can form the same such bonds as any other, and any stretch of backbone could theoretically engage in any such conformation.

Slightly more specifically, the backbone units and some side-groups hydrogen-bond water molecules, and proteins tend to coil in such a way as to present such water-soluble or hydrophilic moieties or groups on their surfaces, and hold those side-groups which cannot form such bonds inside, in water-insoluble or hydrophobic cores.

But in most of the proteins which perform the functions of the cell, conformation is specified by side-group interactions, which depend on the kinds of side-groups available and the order in which they occur, which depend in turn on which amino acids are incorporated into the protein and the order in which they are incorporated.

That is, protein amino acid order determines protein conformation.


Protein Conformation Determines Protein Shape,
Mechanical Properties And Surface Structure

Protein conformation obviously determines protein shape, whether globular, elongated or flattened, and whether solid, indented or hollow; protein mechanical properties, such as whether and how one part of a protein can bend or rotate with respect to the rest; and protein surface structure, the protein’s surface shape and pattern of exposed side-groups and backbone units.


Protein Shape, Mechanical Properties And Surface Structure
Determine Protein Complexing And Function

Two proteins or other large molecules of complementary shape and surface charge-patterns upon being brought together will develop multiple attractions including hydrogen-bonds to one another, such fit and collective attraction being called an affinity and such collective bond a complex.

Protein complexing is so generally specific in its requirements of complementary shape and charge-pattern as to be described as “lock-and-key”.

And protein complexing is a fundamental mechanism of protein function:

The conformation-determining attractions and bonds of and within the protein itself can be considered intramolecular or internal complexing.

Cytostructural proteins complex with one another to form the internal structural framework of the cell called the cytoskeleton.

And every cell contains protein enzymes catalyzing—accelerating—the chemical reactions used by that cell, which reactions would otherwise run too slowly to be of use:

Body cells typically each synthesize thousands of different enzymes, and many molecules of each, each more or less specifically catalyzing its specific reaction operating upon its specific substrate(s) or reactant(s) (the phrase "lock-and-key" was first applied to enzyme specificity). And each enzyme catalyzes its reaction largely through, and its specificity is that of, not so much its complexing with its substrate(s) as with its reaction's rate-determining transition state, the highest-energy state through which that reaction must proceed, stabilizing and therefore lowering the energy of that state, allowing lower-energy passage through that state, increasing the probability that a given enzyme-substrate complex will have the energy needed to pass through that state, and therefore, in the cell or other reaction mixture where many such complexes are forming and dissociating, increasing the number of such able to pass through that state and their reactions proceed to completion at any given time, and therefore the overall rate of reaction.

In addition, many enzymes catalyze water-sensitive reactions in their hydrophobic cores.

More complicatedly, many if not most proteins function by virtue of conformation changes, changing back and forth between two or more conformations in the course and by way of function, a phenomenon called allostery, and complexing is frequently combined in protein function with allosteric conformation changes. Protein complexing of one molecule causing an allosteric conformation change in that protein enabling or preventing subsequent complexing of another molecule is a central mechanism of protein function and control in the cell; for example, some enzymes, including some acting as cell switches, sensors or governors, are activated or deactivated—turned on or off—by conformation changes caused by complexing with or dissociating from the appropriate molecules, some used specifically as signals. And other protein enzymes catalyze the degradation of fuel and use the energy yielded to repetitively alter their conformations and shapes, acting as motors and machines.


Protein Amino Acid Order Determines Protein Function

Protein amino acid order determines protein conformation; protein conformation determines protein shape, mechanical properties and surface structure; and protein shape, mechanical properties and surface structure determine protein function.

Therefore, protein amino acid order determines protein function.

The above is an adaptation from the first chapter of a work in progress, an informal monograph on the empirical or mass trial-and-error development of what the monograph calls "mechanomers", functional copolymers such as the biopolymers, the natural functional copolymers called proteins and nucleic acids; see my condensation of the monograph "Empirical Mechanomeric Development" and two notes on applications from the monograph "Mechanomeric Oncotherapy" and "Empirical Mechanomeric Development and Artificial Photosynthesis of Fuels" .

[See also my new blog EMDblog.]

I am seeking and need a grant or possibly an advance to finish the monograph.

Keywords: empirical mechanomeric development, enzymes, macromolecular nanotechnology, mechanomers, nanobiotechnology, proteins


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