Overview
The main workhorse in our bodies is the cell. A typical human body is comprised of some 30-50 trillion human (eukariotic) cells. This does not include the number of bacteria and viruses, nor any of the other non-cellular body elements and structures. Incidentally, the number of atoms per cell is around 100 trillion. These are average figures and vary as expected per person and per cell.
Each cell is a fascinating collection of billions of components, organized and working together to do the processes that keep us alive and functional. We classify these components into a hierarchy that enables us to understand what we see and what we experience. Visually (under the microscope and based on experiments), the average human cell is composed of a balloon-type membrane that encloses (separates and defines) the cell, and the material inside that bag of liquid that is the cell.
Like we see our body comprised of organs that each do a specific essential task, the cell also contains "organs" that we call "organelles".
The plasma membrane
The plasma membrane is a phrase we use to identify the most common separator in the microbiological world: the thin membrane that englobes the cell nucleus, many organelles and substances inside the cell, and the cell itself. The plasma membrane is a common solution nature found (a protein molecule called a phospholipid) that when present in large quantities naturally forms itself into balloons and thus provides protected volumes of water in which certain processes can flourish without interference from the outside world. Long and thin, one end of the membrane protein is afraid of water (hydrophobic) and the other end loves it (hydrophylic). So when you drop a ton of this protein into water, the proteins naturally configure themselves into spherical clumps. When two clumps meet, they fuse into a larger and larger bubble membrane that encases the water inside the bubble with two layers of this protein (bilayer) - the layers positioning their hydrophylic heads against the water and hiding their hydrophobic tails inside the membrane.
See the wikipedia description http://en.wikipedia.org/wiki/Lipid_bilayer for a pretty good description of the cell plasma membrane.
Fluidity. The membrane is like a viscous liquid. Just to give an idea of the extent, the typical human cell membrane comprises some ? phospholipid molecules, so quite a lot. The important characteristic of this membrane is that the membrane proteins float rather than stick against each other. This looseness allows certain substances to pass through the membrane while preventing others. Very tiny substances like tiny molecules can diffuse directly through the membrane. As well, certain proteins that are compatible can fit into the membrane or squeeze through it. Because of the looseness of the phospholipid molecule envelope, simply pushing against the membrane can bubble off a balloon of the membrane with the balloon enclosing the object that was doing the pushing. Conversely, a balloon that contains elements can fuse with the membrane and thus release its contents into the cytoplasm or, in the opposite direction, into the area outside the cell.
Floating proteins. In addition to this double-layer sea of phospholipid proteins, the cell produces many other types of proteins that live inside or are stuck into the plasma membrane, and the membrane liquidity allows such proteins to naturally move (float) along and around the membrane like life rafts tossed into the sea. The 100s and 1000s of these floating proteins each have specific functions; for example, hairlike strings to keep the cell "bubble" from coalescing with the neighboring cell bubble.
The double-layer of phospholipids is the same substance and composition as for the smaller balloons the englobe the many intra-cellular components, organelles, and other objects inside the cell. Like the all-encompassing cell membrane, the presence and absence of components floating inside the membrane control whether and when and how individual balloons do or don't coalesce into larger balloons. For example, newly created proteins inside the endoplasmic reticulum (ER) organelle push the ER membrane outwards so that the part of the membrane bubbles off the ER and becomes its own balloon containing the new proteins. That balloon migrates and coalesces with other organelle membranes and, in certain cases, coalesces with the cell membrane itself, thus passing the new proteins into the space outside the cell.
Signaling across the plasma membrane
The cell is preprogrammed in its structure and composition to survive and tend to its own needs. However, to function as a component of a larger assembly of cells such as the human body, the cell is like a machine that can be called upon to do multiple functions (create certain proteins (enzymes, hormones, chemicals - that in turn control other processes), to replicate, even die). The body, therefore, has a mechanism to communicate its requirements to the cell. That mechanism is called "signaling": the body signals the cell to do the required things by communicating those requests - i.e., passing the signals - through the cell's plasma membrane.
Mitochondria
Mitochondria are like tiny cells that float around inside the larger cell. In fact, there is a theory that in primordial times the ancestors of our present-day mitochondria were indeed separate organisms that gradually evolved to live inside larger cells rather than fend for themselves alone in the cruel outside world. For example, each mitochondrion has its own tiny DNA to quickly generate the proteins it needs. The two-layer structure of the mitochondria supports the theory that mitochondria were once separate organisms the were absorbed into the human cell: the inner layer being that of the original organism, and the outer phospholipid layer being the bubbled-off portion of the cell membrane that encased the incoming organism as it pushed its way into the cell cytoplasm. Like an organism (or cell), when required for additional energy provision, each the mitochondria DNA can replicate and the mitochondrion can split into two new mitochondria and grow and mature.
The mitochondria are the powerhouse (battery) of the cell. Each mitochondrion processes billions of ADP molecules into higher-energy ATP molecules. The ATP molecules are then released to provide the energy for the multitude of micro processes that sustain life, degrading back to ADP and loose phosphate in the process. The ADP and the extra separated phosphate molecules are transported into the inner compartment of the mitochondria. The broken-down molecules from the food we eat meet up with the oxygen we breathe - in the outer part of the mitochondria - to produce hydrogen ions and carbon dioxide. The hydrogen ions pass through a protein complex (called ATP synthase floating in the inner membrane) into the inner part of the mitochondria and once there, provide the energy that ADP needs to grab another phosphate molecule and become ATP, which is transported out of the mitochondria. Why oxygen you may ask: well, without oxygen each interacton would produce 2 ATP molecules; with oxygen around to slow down the loose electrons, 36 ATPs are created. Figures.
Anyway, the mitochondria are the "stomachs" of the cell. They eat what we digest. Easter is their delight.
Cell protein synthesis
The main function of a cell is to produce organic molecules called "proteins". The type, quantity, location, and other characteristics of the proteins control life in our bodies. Each such different type of protein has its own purpose and function. Many of these proteins are needed to sustain the cell, itself. Many others are needed to fulfil the cell's destiny as part of the family of cells composing the body.
Cell replication
When required, the body can signal cells to divide and thus increase in number. Once the process of replication is initiated, each organelle, especially the DNA, undergo fascinating changes that enable their duplication and the cell's division.
Apoptosis (cell death)
When the body determines that a cell has completed its intended function and is no longer needed, the body can signal the cell to commit suicide.
Molecules and atoms
The amazing thing I find about the microbiology of life is twofold: 1) how incredibly precisely it relies on the exact characteristics of each molecule and atom, and 2) that life would not be possible without such precision.
Each and every, and all, life systems manipulate nature down to the atom and perhaps beyond. I think the manipulation stops at the atom. If there are variations in the structure and characteristics of atoms - for example, even if we find out that no two hydrogen atoms are exactly alike - the life systems we know ignore differences at that level.
Observations, assumptions, extrapolations
So, if we want to have a complete understanding of how things are, we need to delve into the experimental observations, models, and extrapolations at the atomic level. We need to learn about subatomic science. That's a lot of stuff only the greatest minds can grasp and for which Nobel prizes are awarded.
Another thing that amazes me is that, once you delve into the subatomic world, a whole set of unanswered questions arise:
- What creates the stability volumes around an atomic nucleus that capture electrons?
- What holds the atomic nucleus together?
- What is electrical charge?
- Where does magnetism fit in?
- If electrons, and charged particles, accelerate, don't they emit energy? But such particles are always moving in irregular and changing velocities, that is, that are always accelerating. So?
Forces
Two levels of force seem to control the microbiology of life: covalent forces that bind electrons to the atomic nucleus, and a collective overall weak force that controls the interaction between clumped atoms (molecules). That weak force is called van der Waals force (vdWf). The vdWf (my own acronym I use to save space) is the electric force field around an object such as a molecule. Depending on the scientist's preference, and on how you want to define things, there are various types (mainly 3) of vdWf.
The wdWf depends on the shape and composition of the molecule, which can vary over time measured in minimicroseconds. The wdWf, therefore, depends on the position of the molecule relative to other atomic-sized objects near and within range, the characteristics (velocity, composition, wdWf) of those objects within range, and on such factors as temperature (motion) and pressure being exerted on the overall volume of molecules. Temperature and pressure on a volume are forces that control the velocity and proximity of molecules and objects inside the volume, but are forces that we have modeled and whose impacts we can thus understand.
Covalent bonding seems rather straightforward in that we accept the conservation of energy principle, i.e., the 3D configuration of stability areas around the atomic nucleus. This controls the creation of molecules. Once a molecule is created and stable, that is, once the covalent bonding conditions are satisfied, then that stability removes the strong covalent forces, leaving the weak forces in charge.
The two main effects I've detected re the wdWf field around a molecule seem to be: 1) whether the molecules adhere, that is, when and how, and under what conditions, does a substance change state (solid, liquid, gas); 2) how the force fields around each molecule control the flexing and positioning of its own mass of atoms; and 3) how the force fields around each molecule control the flexing and positioning of nearby molecules. Regarding the impact on itself, the molecule has certain physical arrangements that can persist (are stable and define the chemical characteristics) but the wdW forces can still flex and position the molecular configuration, especially for large organic molecules, to stress and polarize even those chemically "stable" configurations.
As described in other chapters of this online document, nature uses effect 2) when creating organic molecules (proteins), and effect 3) when controlling biologic processes (for example, using enzymes).