The Song of the Cell

Every cell in a multicellular organism is surrounded by an oily membrane that separates it from other cells and from the extracellular fluid that bathes all cells. The cell surface membrane is permeable to certain substances, thereby allowing an exchange of nutrients and gases to take place between the interior of the cell and the fluid surrounding it. Inside the cell is the nucleus, which has a membrane of its own and is surrounded by an intracellular fluid called the cytoplasm. The nucleus contains the chromosomes, long thin structures made of DNA that carry genes like beads on a string. In addition to controlling the cell's ability to reproduce itself, genes tell the cell what proteins to make to carry out its activities. The actual machinery for making proteins is located in the cytoplasm. Seen from this shared perspective, the cell is the fundamental unit of life, the structural and functional basis of all tissues and organs in all animals and plants.

Besides their common biological features, all cells have specialized functions:

Liver cells, for instance, carry out digestive activities
Brain cells have particular ways of processing information and communicating with one another. These interactions allow nerve cells in the brains to form complete circuits that carry and transform information

From The Song of the Cell by Mukherjee

Introduction

To be living, an organism must have the capacity to:
- to reproduce
- to grow
- to metabolize
- to adapt to stimuli
- to maintain its internal miliau
Complex multicellular living beings also possess emergent properties, which emerge from systems of cells:
- to defend against injury or invasion
- organs with specialized functions,
- physiologic systems of communication between organs
- even sentience and cognition
It is difficult to imagine life without cells, or to imagine cells without life

A cell is an autonomous living unit that acts as a decoding machine for a gene. Genes provide instructions to build proteins, the molecules that perform virtually all the work in a cell. Proteins enable biological reactions, coordinate signals within the cell, form its structural elements, and turn genes on and off to regulate a cell's identity, metabolism, growth, and death. They are the central functionaries in biology, the molecular machines that enable life.
A cell thus transforms information into form, genetic code into proteins. A gene without a cell is lifeless. A cell brings materiality and physicality to a set of genes. But not only that.
Having unpacked the code by synthesizing a select set of proteins that is encoded in its genes, a cell becomes an integrating machine. It uses this set of proteins (and the biochemical products made by proteins) in conjunction with one another to start coordinating its function, its behavior (movement, metabolism, signaling, delivering nutrients to other cells, surveying for foreign objects) to achieve the properties of life. And that behavior, in turn, manifests as the behavior of the organism. The metabolism of the organism reposes in the metabolism of the cell, And the same for the reproduction, repair, survival, and death of the organism
Finally, the cell is a dividing machine. Molecules within the cell - proteins again - initiate the process of duplicating the genome. The internal organization of the cell changes. Chromosomes, where the genetic material of a cell is physically located, divide, and this division drives growth, repair, regeneration, and ultimately, reproduction, among the fundamental, defining features of life.

The Universal Cell

You have to think of a cell as a functional site for all physiological chemical reactions, as an organizing unit for all tissues, and as the unifying locus for physiology and pathology.
You have to move from a continuous organization of the biological world to a description that involves discontinuous, discrete, autonomous elements that unify the world:
- See past flesh (continuous, corporeal, visible)
- To blood (invisible, corpuscular, discontinuous)

Raspail - "A cell is a kind of laboratory" - it enables physiology
Virchow - "The body is a cell state in which every cell is a citizen."

Tenets of cell theory:

All living organisms are composed of one or more cells
The cell is the basic unit of structure and organization in organisms
All cells come from other cells
Normal physiology is the function of cellular physiology
Disease, the disruption of physiology, is the result of the disrupted physiology of the cell

The Pathogenic Cell

Germ theory - microbes are independent, living cells capable, in some cases, of causing human illnesses
Bacterial cells, Pasteur concluded, are carried in air and dust. Putrefaction or rotting was not caused by the inner decomposition of living creatures - or some visceral form of interior sin. Rather decomposition only happened when these bacterial cells landed on the broth.
Infections were invasions by microbes - single-celled organisms that entered other organisms and caused pathological changes and tissue degeneration

Antibiotics recognize some molecular component of hyman cells that is different from a bacterial cell. They are cellular medicines, drugs that rely on the distinctions between a microbial cell and a human cell.

Every cell on earth belongs to one of three branches:

Bacteria - single-celled organisms that are surrounded by a cell membrane, lack particular cellular structure found in animal and plant cells and possess other structure that are unique to them.
- They are ferociously successfully and dominate the cellular world. Not just pathogens - our skin, guts, mouths are teeming with several billion bacteria that cause not disease whatsoever. Humans are just "nice-looking luggage to carry bacteria around the world".
- They live in the hottest and coldest parts of the world. They are autonomous, mobile, communicative, and reproductive
Eukaryotes - cells containing a nucleus, which is a storage site for chromosomes (bacteria are prokaryotes - before nuclei).
- We and other eukaryotes are feeble, finicky beings capable of living in vastly more limited environments and restricted ecological niches
Archaea - They look like bacteria, are tiny and lack some of the structures associated with animal and plant cells. Recently established as a separate domain, we know relatively little about them

The history of the cell:

The first cells arose on Earth some 3.5-4bn yeats ago, about 700m years are the birth of the Earth.
The simplest cell (a protocell) had to possess a generic information system that could reproduce itself. This was probably made of RNA.
Two RNA molecules were probably needed - a template and a duplicator - and they had to avoid separation, so some sort of structure - a spherical membrane, was likely needed to confine them. These three components may have been the first cell
At first the RNA would duplicate within the confines of the sphere, but at some point it would grow too big and split in two.
Then evolution would select more and more complex features of the cell, eventually replacing RNA with DNA as the information carrier.
Bacteria evolved out of that simple progenitor about 3bn years ago and they continue to evolve today. Archaea are probably at least as old as bacteria
About 2bn years ago, evolution took a strange and inexplicable turn, when a cell that is the common ancestor of human cells, plant cells, fungi cells, animal cells, and amoebal cells appeared on Earth.
This ancestor was recognizably a "modern" cell, with an exquisite internal structure and unprecedented molecular dynamism, all driven by sophisticated nanomachines encoded by thousands of new genes that are largely unknown in bacteria.
New evidence suggests that this "modern" eukaryotic cell arose within archaea, so that we are a relatively recent sub-branch of archaea.

The Organized Cell

The membrane:

Has two layers of lipids
Proteins are embedded in the membrane, like hatches or channels

The protoplasm/cytoplasm:

is a mind-bogglingly complex soup of chemical
It has a molecular "skeleton" that maintains the form of the cell and is called the cytoskeleton. It is made of actin and tubulin which form tubular structures and tethers components of the cell together.

The ribosome:

Is a massive macromolecular structure, a multipart assemblage.
It captures RNAs and decodes their instructions to synthesize proteins

Proteins:

Are the workhorses of the cell.
they create structural components, are receptors for signals from outside, form pores and channels across the membrane, and are the regulators that switch genes on and off in response to stimuli.
Building proteins is one of the cell's main tasks.

Organelles:

Are mini organs found inside cells

The mitochondria:

Are organelles that are the cells fuel generators - maybe originally microbrial cells that developed the capacity to produce energy via a chemical reaction involving oxygen and glucose, and which were engulfed or captured by other cells:
They are found in all cells, but are particularly dense in muscle cells, fat cells, certain brain cells, and other cells that need the most energy or regulate energy storage.
They are wrapped around the tails of sperm to provide swimming energy. They have no autonomous life and can live only within cells.
They produce energy through an aerobic reaction, breaking down sugar and feeding the result into a cycle of reactions to make ATP (adenosine triphosphate), which is the central currency of energy in virtually all living cells. There is a faster, but less efficient anaerobic production of ATP, which happens directly in the protoplasm.

The endoplasmic reticulum (ER):

Is an organelle that is a maze of winding, tortuous pathways.
Acts as a postal system. RNA is translated into a protein by the ribosome and then pushed into the ER, which sends it to the Golgi apparatus, which routes it to its final destination in the cell

The nucleus:

Is an organelle that is found in all plant and animal cells (but not in bacteria)
Is the storage bank for DNA, for the genome
Proteins enter through the pores of the nuclear membrane and bind to the DNA and turn genes on and off.
The set of on/off genes instructs a neuron to be a neuron and a white cell to be a white cell.
During the development of an organism, genes - or rather proteins encoded by genes - tell cells about their relative positions and command their future fates.
Genes are turned on and off by external stimuli such as hormones, which also signal changes in a cell's behavior.

Claude Bernard in the 1870 shifted physiology's focus from action to the maintenance of fixity. A major point of physiological activity, paradoxically, was to enable stasis. Don't just do something, stand there! - homeostasis.

The Dividing Cell

Every cell is the product of birth from another cell
Not every cell is capable of reproducing - some cells, such as neurons, have undergone permanent division and will never divide again
Mitosis (from the Greek for thread) is the process of dividing to produce new cells to build organs and tissues
Meiosis (from the Greek for lessening) is the birth of new cells, sperm, and eggs for the purpose of reproduction - to make a new organism
The lifecycle for a multicellular organism is a back and forth between meiosis and mitosis:
- Humans start with 46 chromosomes in every bodily cell and produce sperm cells in the testes and egg cells in the ovaries via meiosis, each ending up with 23 chromosomes
- When sperm and egg meet to form a zygote, the number of chromosomes is restored to 46
- The zygote grows through cell division, mitosis, to produce the embryo, and then develops progressively mature tissues and organs - heart, lungs, blood, kidneys, brain - with cells that have 46 chromosomes each
- As the organism matures, it eventually develops a gonad (testes or ovaries), with 46 chromosomes in each cell
- When the cells in the gonads make male and female reproductive cells, they undergo meiosis, generating sperm and eggs with 23 chromosomes each
- Fertilization restores the number to 46. A zygote is born and the cycle repeats. Meiosis, mitosis, meiosis. Halve, restore, grow. Halve, restore, grow.