Bil 255 - Journey to Cosmos of the Cell

Properties of Life via a Journey to Cosmos of the Cell


Empedocles (490-430 BC) argued everything including Life is made up of 4 eternal "elements":
                                     earth,     air,     fire     &     water.
Aristotle (384-322 BC) divided the world into 3 major groups:
                                     animal,   vegetable,   &   mineral.
today, we know Cells are the unifying Concept of all LIFE... the unity of Biology...
                    & CMB is the study of the Molecular Chemistry of Cells...



  a CELL is the fundamental unit of LIFE... (just as an atom is a fundamental unit of matter...)

1st           "life is an inanimate mixture of biomolecules selected
                 for their fitness to perform certain biochemical
                 reactions that characterize and define life".       a 2nd definition

Every living thing is cellular…
           "The only life we know for certain is cellular..."
                                                  H.J. Morowitz - biologist & philosopher

    all the class reading assignments for this section on cells are in the class web pages







WHAT IS YOUR PERSONAL VIEW or YOUR WAY of DESCRIBING LIFE ?
                    Think about of what you would have to include in your Definition of Life*

Most biologists agree:    life exhibits certain "QUALITIES" that equate to the living state
and many prefer to use an operational definition of What living entities CAN DO and
Perform rather than to use a strict definition of life thus...

Let's look at the...   ATTRIBUTES of the LIVING CONDITION    what cells & life Can DO.

1) Autonomous Replication - Self-Replication of cells [cell division - Mitosis & Meiosis
           PICS* (review panel 18-1 pages 628-629 on mitosis)
                        microscopic observations*   +    chromosome motions*
    - all cells store their hereditary information in DNA, coded as genes.
    - two whole genome copies: maternal & paternal hereditary info = BACKUP-REDUNDANCY
    - copied by universal replication of DNA mechanism (complementary templated polymerization)...
           ►  self replication may be the most defining trait of the living state…

2) Life begets Life - a prime directive of life.
           ► Prime Directive:    Rudolph Virchow states (1858) the Biogenic Law:
                     Omnis cellula e cellula...    "all living cells arise from pre-exisiting cells"
               All individual cells in an organism are descended from one fertilized egg.
               This hypothesis negates Spontaneous Generation - Redi & Pasteur experiments*






3) Life has an Evolutionary Origin - "all living things have evolved from a common ancestral cell ",
    thru processes including natural selection & genetic drift acting on heritable genetic variation.

   ► LUCA - Last Universal Common Ancestor* is the most recent population of organisms
                                   from which all organisms now living on Earth have a common descent.

    SUPPORTING EVIDENCE ...
           the hypothesis that all cells are derived from a primordial cell is mostly based upon the
           circumstantial evidence, due to the commonality that occurs in all known living cells:
    such commonality as...
       1. all living things are composed of very similar organic molecules:
               the same proteins, lipids, carbohydrates, & nucleic acids (DNA & RNA), etc...

       2. all proteins, the biological catalysts responsible for life's chemical reactions,
               are made from one set of 20 standard amino acids... α-amino acids & L-stereoisomers...

       3. all contemporary organisms carry their genetic information in nucleic acids [DNA/RNA]
               and use the same genetic CODE.













  4) Life exhibits EMERGENT PROPERTIES...  large scale, complex group behavior in a system,
        which doesn't seem to have any clear explanation in terms of the system's constituent parts.
            ex: metal Na is explosive & gas Chlorine is poisonous --> edible table salt NaCl*
                          ex: oxygen - colorless, odorless, tasteless, reactive GAS that supports combustion
                   hydrogen - colorless, odorless, tasteless, reactive GAS that is flammable
                             water - H₂O - a non-flammable chemically reactive polar LIQUID that exists in 3 phases
       Emergent properties are unexpected, nontrivial results of relatively simple interactions by
           relatively simple components. Emergent properties seem to be a consequence of complexity
           from which unpredicted behaviors and patterns emerge [individual organs give rise to an organism].

5) Life requires a Critical Level of molecular COMPLEXITY to exhibit emergent properties...
          Structural complexity and information content are built up according to current paradigm
          by combining simpler subunits into multiple complex combinations.
              elements > monomers > polymers > metabolism > organelles > cells*
                  number of component parts in cell (E. coli) vs. a computer*

►   from a mix of biomolecules thus emerges a complexity that exhibits properties we call Life:

          Individual molecules have no concept of whole cell; a single cell has no concept of the whole.
          A cell runs by chemical rules built into its molecules. A single cell can't do much without
          interaction with other cells, but in combination cells can produce complex interactions,
          such as consciousness.


  6) Life exhibits biochemical autonomy, i.e., it carries on & regulates its own METABOLISM:
sum of all chemical reactions in living organisms
      Cellular metabolism occurs via a few basic molecular reaction mechanisms common in all cells...

                                1. cellular redox reactions^-...   (gaining / losing electrons),
                                2. capture of light energy......   (electrons) in photosynthesis,^-
                                3.   electron transfers..............   (e^- flow through carrier proteins),
                                4. H⁺ion pumps ...................    (ATP synthase = a proton gradient)^-
                                5.   concentration gradients....   across membrane interfaces.^-

       these reaction mechanisms transform molecules & energy to sustain living cells,
     often by making and/or using ATP* .

   Life is a chemical system far from equilibrium...
           ► it consumes free energy, largely derived from photosynthesis, which is stored in
                high-energy bonds* or ion concentration gradients*.
                  Cells use gradients as an energy source.
            ► The release of this energy may be coupled to thermodynamically unfavorable
                  reactions to drive biological processes & keep reactions from approaching equilibrium:
                  ability of cells to couple reactions* (non-favored to favored) is a unique property of life.

Remember there are no unique Laws of chemistry or physics just for the Living State...

7) Life may also manifest by the absense of the living condition...
        The absence of life (dead cells) is in common with non-living things,
                 but a lack of the properties of Life is in itself not definitional of living state.
        The, the fact that living things have an ability to die is somewhat defining.

     Cells DIE - when metabolism ceases & complexity collapses with no prospect of starting again.

            "Cell Death... is the collapse of the quantum state which has allowed living matter to take
        energy from the environment, while preventing an increase in local entropy and delaying
        the tendency of energy to be dispersed or diffused".
   The 2nd Law of Thermodynamics may be the 1st law of Life: If you do nothing, entropy will move you to
               a higher State of Disorder that ends in Death. So, a basic ability of life is to combat Entropy by
               being chemically "extropic" - expending energy to survive and flourish. Entropy will disorder (end)
               the Universe in the long run, but the living state is in the 'now', so we study, learn, and do our duty
               to stave off equilibrium.

    ► LAW OF ENTROPY CAN BE TEMPORARILY BLOCKED (i.e., Life),
     (often by coupled reactions), BUT ENTROPY CAN NEVER BE VIOLATED.


          Cell death, the absence of the attributes of life, is different than Cell Senescence,
              which is a process of aging, a phenomena where isolated cells show limited ability
              to continue to divide, i.e., to age.

                   within each cell cycle is also believed to influence the vitality of the cell, thus contributing.

The successive shortening of the chromosomal telomeres

so then.... What is it that makes a Cell Alive???? Is the 'universal' DNA alive? Cellular life does emerge from DNA, but is DNA itself alive? probably not; DNA appears inert until it becomes 'animated'. What stimulus animates DNA? maybe Brownian motion & Laws of Thermodynamics bootstrap DNA, as the DOS of a cell? The term "Life" has a very unique definition, not observable at the DNA level, thus we often say that viruses are neither dead nor alive, but just are Biochemical entities.
Single cells are also biochemical, but they may also exhibit reactions which are mostly unpredictable, often showing emergent properties. ex: amoebas*, all with the same DNA and molecular makeup, can each move in many different directions, rather than all responding in the same direction... i.e., they exhibit many different biochemical responses in the same environment.
Multicellular (aggregate) life may form many diverse responses as they seek to survive... Evolution disposes of aggregate organisms that do not exhibit survival conditions, and
Religions tells us that Entities (Humans) have a Spirit that is not of matter??? but that is a topic that is not treatable by the Scientific Method.
a wild speculation... is Life a a computer simulation? pic? not likely (for the future)?.

So then we define Cells (and Life) by what it does...

      i.e., What are the properties that make Cells Alive:

      cells obey the Laws of Chemistry & Physics (Laws of Universe) including...
    cells build and degrade numerous molecules, generally via energy transformations...
      cells transform energy from environment, yet maintain a homeostasis far from equilibrium...
      cells transform and capture energy via metabolic pathways: as Glycolysis, Krebs, ATP...
      cells metabolize - capable of 1,000's of reactions (via Enzymes in metabolic pathways)...
      cells are capable of self regulation - series of ordered reactions that are self-adjusting...
      cells osmoregulate - control what gets in/out of membranes (organelle or plasma)...
      cells are motile.- and involved in manymechanical activities of assembly, disassembly,
                movement of organelles using Motor Proteins*
      cells respond to stimuli via receptors and signal molecules... fig 16.8*
      cells grow and divide...
               use nucleic acids for genetic information
               are capable of self-replication via Mitosis & Meiosis
               regulate their gene expression (RNA and protein synthesis)
               differentiate to establish form & shape.
   * read this
- Back to Bb    next - Origins of Life.





PLEASE IGNORE THE MATERIAL & LINKS BELOW...


     pre-programmed cell death is known as... apoptosis via cysteine-aspartic acid (caspases)

   LIVE CELL ?


[a genome browser]


            ΔG   =   ΔH - T ΔS (Gibbs Free Energy Equation)


            cell death plays a role during physiological processes of multicellular organisms,
          particularly during embryogenesis and metamorphosis... i.e., mouse paw apoptosis-18.35,

     [Cells Alive - diagram animation of cell structure]