"Biochemistry"

• The field that deals with the chemistry of biological systems

"Chemistry"

• The exchange, transfer or rearrangement of electrons between or within a molecule or atom(s)
• Chemical bonds between atoms represent the sharing of electrons, therefore, chemistry concerns the breaking and forming of bonds between atoms and molecules
• Electrons are attracted to the nucleus (opposite charges attract), therefore, chemistry as we have defined it is associated with electrons, atoms and molecules trying to achieve a low energy configuration

"Biological System"

• Complicated and organized (low entropy)
• Hierarchy of structure:

Atoms à Molecules à Macromolecular assemblies à Organelles à Cells

• NOTE: only at the level of cells do we have "Life" (atoms, molecules, macromolecular assemblies and organelles are not considered "living"

• Biological structures have a function or purpose
• True at various levels of organization within the living system:
• ATP is a "high-energy" molecule, and can be used to drive energetically unfavorable reactions necessary for the maintenance of a living system
• The large macromolecular assembly known as a ribosome functions to translate the information in an RNA molecule into a protein
• A nerve cell can function to communicate information within a living system
• The heart as an organ in a living system functions as a pump for the blood
• Living systems require energy input to perform work and produce complex structures from simple molecules (reduction in entropy)
• Living systems are able to self-replicate
• They have information-storage molecules (DNA/RNA). Often, these molecules are actively repaired.
• Replication is not entirely precise, thus, variations are introduced

Two common statements you may have heard about "Life":

• Life requires liquid water
• Life is carbon-based

Water is a compound, that is liquid between 32°F (0°C) and 212°F (100°C) and has an amazing ability to solubilize a variety of molecules and ions.

Life is Carbon-based

Life requires complex assemblies and complex molecules to achieve unique functionalities

• We can answer this question to a certain extent by asking an alternative question, why aren't living things composed of noble gases or of metals (noble gases comprise the right-hand group in the periodic table, and metals comprise the majority of elements in the periodic table; non-metals being on the right-hand side)?
• Noble gases have an octet of valence electrons, and as such, don't share electrons and don't form covalent bonds. They exist as single atoms and cannot form complex molecules. At sufficiently cold temperatures they may form a liquid, but that's about the extent of their ability to form complex arrangements of molecules. Little, if any, ability to react chemically.
• Metals have more than an octet (either 1, 2 or 3 extra valence electrons). They have a low ionization energy and prefer to simply oxidize yielding a cation form which does not form any chemical bonds
• What about Group 7 (halogen) elements?
• These are one electron short of a valence octet. They prefer to form a single bond with another element, often forming a diatomic halogen compound. Thus, complex molecular structures based on halogen elements are not possible; single bonds are the limit of their complexity
• The benefits of Carbon
• Four valence electrons means it can form four bonds. These would be tetrahedral in geometry. The ability to form double and triple bonds means that a wide variety of other geometries are possible (trigonal planar, linear)
• The electronegativity of Carbon is approximately intermediate between other non-metals. Thus, polar bonds can be formed with carbon where the other non-metal has either a partial positive or negative charge. Thus, in combination with the available molecular geometries of carbon, both polar and non-polar molecules can be formed, and a variety of partial charges can reside in different locations within the molecules
• Pure Carbon is not water soluble. It is the covalent bonding with other elements with significantly different electronegativities (e.g. O, N) that allow carbon compounds to be soluble
• Compounds with high carbon content tend to phase-separate from water (e.g. gasoline)
• The Bottom Line
• Complex molecules of carbon can be constructed, and with a variety of polarities, charges, chemical reactivities and physical properties

"Minimal" media for bacterial growth

Living systems are characterized as being able to use energy to overcome the entropic cost of assembling complex macromolecules from simple chemical compounds. Many bacteria can grow on the following media (known as "minimal" or "M9" media):

Cations:

• Na⁺ (required for osmotic pressure, ion transport, enzyme function, etc.)

• K⁺ (required for osmotic pressure, ion transport, enzyme function, etc.)

• NH₄⁺ (nitrogen source for proteins, nucleic acids, some carbohydrates, etc.)

• Mg²⁺ (required for function of enzymes, nucleic acids, etc.)

• Fe²⁺ (required for function of electron transport complexes, etc.)

Anions:

• PO₄^3- (phosphorous source for nucleic acids, some proteins, high energy molecules, pH buffering, etc.)

• Cl^- (required for osmotic pressure, ion transport, etc.)

• SO₄^2- (sulfur source for proteins, electron transport complexes, etc.)

Carbon source:

• Any compound like glycerol or glucose (i.e. carbon in a soluble, reduced form). A source of carbon for proteins, nucleic acids, lipids, carbohydrates. A source of reduced electrons for energy production

The composition of Living systems

• C, H, O, N elements (non-metals) comprise 99.4% of the elements in living systems
• The earth is mostly O, Si, Al and Fe
• C, H, O, N are produced in almost every star (
contemplate the fact that there are ~100 billion stars in our galaxy and ~100 billion galaxies in the universe). Only much larger stars produce heavier elements, and elements heavier than iron require a super-nova for formation.
• For more information on nucleosynthesis (i.e. how atoms are made in stars)
click here!

• The sun's dual role in living systems
- provides the energy for living systems and produces and distributes the elements necessary for living systems
• Carbon's dual role in living systems
- provides the chemical structures essential for complex biological molecules, and is also the source of electrons for the energy that living systems require. Sort of like a gingerbread house...

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