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Chemical Context of Life
MATTER occupies space and has mass
The kinds of matter that make up everyday objects including rocks, paper clips and frogs, are composed of elements.
ELEMENTS can’t be broken down into other substances by chemical reactions. There are 90 odd; ex: H, O, Fe, Au
COMPOUNDS are substances composed of two or more elements. Ex: NaCl
25 elements are known to be essential for life.
C, O, H and N make up 96% of living matter.
P, S, Ca, K, Cl, Na, Mg, and Cl account for most of the rest.
Fe and Cu are the most abundant heavy metals, but Zn, Co, Mo, Mn and Ni are also important.
Trace elements include I (thyroid) 150 ug
Element’s physical and chemical properties are determined by atomic structure
Atoms are composed of neutrons and protons (heavy) and electrons (light)
Neutrons (neutral) and protons (positive charge) make up the nucleus; in neutral atoms # electrons = # protons
Atomic mass ~ Neutrons + Protons (each weigh about 1.7X10-24 grams); electron mass is negligible in atomic mass (10-27 grams).
Atomic number is just the # of protons, and this determines chemistry
Many elements exist as several ISOTOPES with different masses but the same atomic number. They have the same # of protons but different numbers of neutrons. Isotopes are chemically identical. Some are unstable and break down spontaneously (radioactive). Ex: 12C and 13C are stable, but 14C breaks down 14N. Radioisotopes are important in biology and medicine.
Positively charged protons in the nucleus create an electrical field which attracts the negatively charged electrons.
Unlike satellites circling the earth, there are a limited number of stable states for these electrons. We call these ORBITALS, and they are governed by quantum mechanics.
Atoms can be built up by inserting electrons one at a time into the lowest energy unfilled orbital.
What are orbitals? They are the solutions to differential equations which are specific for the electrical field set up by the nucleus; there are only a limited number of solutions, characterized by numbers (quantum numbers): N, M, and L. Shells are groups of orbitals with the same value of N.
The lowest orbital (the 1s orbital, because N=1) is spherically symmetric and can hold two electrons. Hydrogen is 1s1, and helium is 1s2. There are no other N=1orbitals.
The Octet Rule:
In general, atoms are most stable when they have 8 electrons in their outer-most shell. (Octet means 8.) The exception is the first shell which is most stable with TWO electrons. (Like helium).
HOWCOME?
The n=1 shell had only one orbital, for which m=0. The n=2 shell has a similar orbital, the 2s orbital, for which m=0, which can accept two more electrons (as in Li & Be). There are also three dumbell shaped orbitals, the 2p orbitals, for which n=2, m=1 and L= -1, 0, and +1. Filling these one electron at a time gives the elements B, C, N, O, F and Ne. Neon is very stable because it has a filled shell. Note that it takes 8 electrons to fill the 2s and 2p orbitals.
The N=3 shell has s and p orbitals, but in addition there are five new d orbitals which can accept 2 electrons each. These give rise to the properties of transition metals like iron and copper.
Filling the 3s and 3p orbitals gives the noble gas argon; this takes another 8 electrons. The 4s orbital gets populated before the 3d orbitals are filled.
The result of this aufbau buiding of elements is the periodic table.
Bonds: bonds are interactions between atoms which result in sharing or transfer of electrons to produce low energy configurations.
In ionic bonds, charged atoms attact. Example: In NaCl. Na is the stable positive ion and Cl is the stable negative ion. This allows both to have filled outer shells.
In covalent bonds, electrons are more or less equally shared. Example: in diatomic hydrogen, the two electrons get combined in a molecular orbital. (bonding orbital)
Weak Bonds
Hydrogen Bonds form between an H atom covalently bonded to an electro negative element and a negatively charged atom, usually O or N. The H atom gains a partial positive charge because the electronegative element partially withdraws an electron. H bonds are not just electrostatic in character, but behave like very weak partly covalent bonds.
Van der Waals interactions are very weak interactions between uncharged atoms. Although the atoms are neural overall, fluctuations in electron density lead to transient regions of opposite charge (dipoles). A dipole on one atom can induce an attractive dipole on a nearby atom, leading to very weak, short ranged attractive forces.
Molecular shapes
The shapes of small molecules are almost entirely determined by shapes of the atomic orbitals and the molecular orbitals generated by combining them.
Atoms that form strong covalent bonds rearrange their electrons into hybrid orbitals to minimize the energy of the resulting molecules by making stronger bonds.
Carbon has a strong tendency to use its 2s and 2p orbitals to form four tear drop shaped sp3 orbitals. These orbitals are spread at angle of 104.5 degrees, and as a result molecules like CH4 are tetrahedral in shape.
In water, two such hybrid orbitals of oxygen form bonds with hydrogen atoms, resulting in a V shaped molecule. In liguid water and ice, the two other orbitals are potential H bond acceptors.
In biology, molecular shape is critical in the recognition of molecules.
Receptors recognize molecular signals by their shape because they have binding sites that match. Examples: Endorphins/morpine, sterioid hormones, insulin.
Antibodies recognize antigens largely by shape.
As we will see, enzymes recognize their substrates and cofactors largely by shape.
Processes that make and break chemical bonds, converting one group of compounds to another, are chemical reactions.
Life at the chemical level consists of very specific, highly controlled reactions. They produce the building blocks of living material, and supply the energy needed for life processes.
