What is Life?

I. Characteristics

A. Metabolism:

1. catabolism: harvest energy contained in matter (usually biomolecules but not always; the chemosynthetic bacteria harvest energy by reducing HS In any event, the energy that is harvested is in the form of chemical bonds

2. anabolism: using the energy to build new molecules important to the structure and function of the living unit. But what to build? DNA codes for the structure of particular proteins, which are structural, transport, and enzymatic.

3. Coupled reactions: catabolic reaction break things down, providing energy and substrates for anabolic reactions that build things up.  Actually, the process invovles an intermediate 'energy currency' - ATP, and two sets of coupled reactions.

4. Reactions are constrained by the 1st and 2nd laws of thermodynamics:

B. Growth: Just a consequence of storage of matter > loss (or catabolism).

1. Cell Growth - increase in cell mass

2. Organismal growth: cell growth cell division and an increase in the number of cells allows for cell specialization in function, and greater efficiency.

C. Reproduction:

1. Cell reproduction = division. Must double material, then divide it evenly.

2. Organismal reproduction:

D. Response:

Must respond to the environment physiologically, behaviorally, evolutionarily (genetically)

E. Evolutionary History

1. The passing of DNA from parents to offspring creates patterns of relatedness

2. The patterns of relatedness occur within families, among families, within species, and between species.

3. Thus, similarity in DNA can be used to reconstruct these patterns - phylogenies. For instance, the human chimp, gorilla triad.

F. Life is Cellular

1. Why Cells?
     - boundary separates the environment from life processes in the cell - allows the cell to be differnt from the environment, accumulating some things at higher concentration and eliminating other things.

2. Why are cells small?
     - As objects increase in size, SA increases as a squared function of length but volume increases as a cubic function of length.  So, volume increases faster than SA.  So, the SA/V ratio decreases as an object increases in size.  For a cell, the SA represents the rate at which nutrients can be absorbed and wastes can be expelled - because nutrients and wastes must cross the SA to get in or out.  But the volume is where the reactions occur - the volume represents the metabolic potential of the cell.  So, as a cell increases in size, the metabolic potential (and demand for nutrients) outpaces the rate of supply (relative to the SA). The cell becomes less efficient.

    - Cells are dependent on reactions between small chemicals.  The rate of reactions is affected by the concentration of the reactants.  It is easier to raise concentrations to reactive levels in a small space than in a large space.

II. Levels of Biological Organization

READ THIS. YOU WILL BE RESPONSIBLE FOR KNOWING THE ORDER OF THESE SCALES. FOR INSTANCE, YOU WILL NEED TO KNOW THAT ATOMS ARE SMALLER THAN MOLECULES THAT ARE SMALLER THAN CELLS. Biological systems are complex, regardless of their size. This complexity is required to maintain the system against the tendancy of matter and energy to decay to a more disorganized state (increase in entropy - second law of thermodynamics). Biological systems span an incredible range of spatial and temporal dimensions. Here are some lists to put these concepts in perspective.

A. Spatial Scales of Biological Systems (^ = 'to the power of' (exponent follows))

1. Biosphere: Earth is 1.27 x 10^7 m in diameter (10,000,000 m) ~4 x 10^7 m in circumference
2. Ecosystem: drop of pondwater with algae and zooplankton (1 x 10^-3 m) to Amazon Rain Forest (5 x 10^6 m across; about 1/10 of Earth's circumference).
3. Community: equally variable
4. Population: equally variable
5. Individual: Smallest Mammal - Pygmy Shrew: 2 inches (5 x 10^-2 m) Largest Animal Ever - Blue Whale: 100 feet (30 m) Longest Dinosaur - Seismosaurus - 28 m (estimated) Human - 6 ft... 2 m
6. Organs: variable
7. Cells: variable - Liver Cell: 2 x 10^-5 m (2/100ths of a mm) E. coli Bacterium: 2 x 10^-6 (1/10th of a liver cell) Virus: 2.5 x 10^-8 (1/100th of a bacterium) 8. Organelles: Ribosome: 1.8 x 10^-8 m Mitochondrion: 2.5 x 10^-6 m (about bacteria sized)
9. Molecules: Hemoglobin (average protein): 6.8 x 10^-9 m (1/1000th of a bact.) Phospholipid: 3.5 x 10^-9 m Glucose: 7.0 x 10^-10 m Amino Acid: 5.0 x 10^-10 m
10. Atoms: Carbon: 1 x 10^-10 m (1/10,000,000,000 m - a ten billionth of a meter) (a ten millionth of a millimeter) (a ten thousandth the length of a liver cell) 11. Nucleus: 2 x 10^-15 m. So, the nucleus is only 1/50,000th the width of the atom. Atoms are mostly space. In fact, a cubic centimeter of nuclear matter (no space) would weigh 230 million tons (Physics by J. Orear, 1979) Analogy: If a basketball 1 ft. in diameter represents the nucleus of an atom, the edge of the electron cloud would be about 5 miles away in either direction; the atom would be 10 miles wide. That's a lot of volume. Analogy: You and the Earth are separated by 7 orders of linear magnitude. A millimeter, about the size of this bold-faced period . and a carbon atom are separated by 7 orders of linear magnitude. So, to a carbon atom, the period is it's Earth.... mind blowing... Cells make up living systems that can be 12 orders of magnitude larger (cell to biosphere).

B. Temporal Scales

1. Age of Earth: 4.5 x 10^9
2. History of Life on Earth: 3.5 x 10^9 years (3.5 billion)
3. Oldest Eukaryotic (nucleated) Cells: 1.8 x 10^9 years (1.8 billion)
4. Oldest Multicellular Animals: 6.1 x 10^8 (600 million)
5. Oldest Vertebrates: 5.0 x 10^8 (500 million)
6. Oldest Land Vertebrates: 3.6 x 10^8 (360 million)
7. Age of Dinosaurs - Mesozoic: 240-65 million
8. Oldest Primates: 2.5 x 10^7 (25 million)
9. Oldest Hominids: 4.0 x 10^6 (4 million)
10. Oldest Homo sapiens: 2.0 x 10^5 (200,000)
11. Oldest Art: 3.0 x 10^4 (30,000; 1/100,000th of Life's History)
12. Oldest Agriculture: 1.0 x 10^4 (10,000)
13. Oldest Organism: Bristlecone pines: 5 x 10^3 (5000 years)
14. Human cell: variable - brain/muscle 7.0 x10^1 (70 years) - Red Blood Cell - weeks - Skin cell - days
15. Supply of ATP in cell - 2 seconds
16. rates of chemical reactions - milliseconds (3.1 x 10^10 milliseconds/year). The history of life, spanning billions of years, is dependent on reactions that occur at a temporal scale separated by 19 orders of temporal magnitude.

Atoms and Bonds

I. Atoms

A. Matter

    1. Elements are different forms of matter which have different chemical and physical properties, and can not be broken down further by chemical reactions.
    2. The smallest unit of an element that retains the properties of that element is an ATOM.

B. Properties of Atoms

    1. Nucleus (protons (+) and Neutrons (0).  The number of protons distinguishes one element from another (Atomic number).
    2. Cloud of electrons (-) Shells and orbitals: Shells 1, 2, 3 have 1, 4, 4 orbitals, holding 2, 8, and 8 electrons Distance of orbital correlates with energy of electron farther away from nucleus, more energy. Electrons can absorb or release energy and move to an outer orbital or inner orbital. Without an input of energy, an atom will lose energy and approach it's lowest energy state. Binding properties are largely governed by the number of electrons in the outermost orbital.
    3. Mass = # protons + # neutrons.
    4. Charge = number of protons relative to number of electrons If unequal, then the atom has a net charge and is called an ion.
    5. Space: The orbitals are 10,000 x the width of the nucleus, so an atom is mostly space
    6. Radioactive Decay:
            Isotopes: Isotopes are atoms with extra neutrons...thus they are heavier.  Some isotopes are stable; others decay (lose the extra neutrons). Radioisotopes (those that decay) emit energy (radiation) when they loose a neutron. This change in the nucleus is unaffected by environmental conditions (chemical reactions, temperature, etc.), and thus the rate of decay is constant. Since the rate is constant, if we can measure the amount of parent and daughter isotopes, and we know the rate of change, we can determine the amount of time that has passed for "this much change" to occur.

            Gamma decay -   neutron emits energy as a photon - no change in neutron number, mass, or element.
            Alpha decay - loss of an alpha particle  (2 protons and 2 neutrons) from the nucleus.  This changes the mass and element.
                    (Uranium with 92 protons decays to Thorium with 90 protons)
            Beta decay - a neutron changes to a proton, and an electron is emitted. This changes only the element (determined by the number of protons.), but not the mass.
                    (C14 is an example here... with the conversion of a neutron to proton N14 is produced)

                a. Principle:
                   - measure amt of parent and daughter isotopes = total initial parental
                   - with the measureable1/2 life, determine time needed to decay this fraction
                   - K40-Ar40  suppose 1/2 of total is Ar40 = 1.3by

                (Now, you may be thinking, "be real"! How can we measure something that is this slow?)

                 - Well, 40 grams of Potassium (K) contains:
                                 6.0 x 1023 atoms (Avogadro's number, remember that little chemistry tid-bit?).

                  So, For 1/2 of them to change, that would be:
                                 3.0 x 1023 atoms in 1.3 billion years (1.3 x 109)

                  So, divide 3.0 x 1023  by 1.3 x 109 = 2.3 X 1014 atoms/year.

                  Then, divide 2.3 x 1014 by 365 (3.65 x 102) days per year = 0.62 x 1012 per day ( shift decimal = 6.2 x 1011)

                  Then, divide 6.2 x 1011 by 24*60*60 = 86,400 seconds/day: (= 8.64 x 104) = 0.7 x 107 atoms/second

                   0.7 x 107 = 7 x 106 = 7 million atoms changing from Potassium to Argon every second!!!

                 This radiation is detectible and measureable...and when it has been measured over the last 100 years, it is always the same.  So, not only is there theoretical justification for expecting a constant decay rate, tests have confirmed this expectation. It is unaffected by any known physical change in the environment... freeze it, heat it, pressurize it... no change in the rate of decay. Again, the age of the Earth was not determined by evolutionary biologists... the age of the earth was determined by atomic physicists. And these same principles are APPLIED in the nuclear reactors that provide our electricity. Apparently we have a pretty good handle on how this works, and that this is "correct" at a very high level of probability.
 

Study Questions:

1. List six characteristics of living systems.

2. Describe the relationhsip between catabolic and anabolic reactions, including why they are coupled and how the laws of thermo apply.

3. Why are cells small? Describe two reasons.

4. Put these levels of biological organization int heir proper scalar sequence from small to large: cell, organelle, molecule, tissue.

5. Distinguish between these terms: element and atom.

6. Distinguish the three types of radioactive decay.

7. Suppose we have an Ar40:K40 ratio of 3:1..... and the 1/2 life is 1.3 billion years... how old is the rock? (Assume that Ar40 is ONLY produced by decay from K40... which is correct).