Overview: Chemical Foundations of Biology

Living organisms and the world they live in are su’bject to the basic laws of physics and chemistry.
Biology is a multidisciplinary science, drawing on insights from other sciences.
Life can be organized into a hierarchy of structural levels.
At each successive level, additional emergent properties appear.

Concept 2.1 Matter consists of chemical elements in pure form and in combinations called compounds

Organisms are composed of matter.
- Matter is anything that takes up space and has mass.
- Matter is made up of elements.
An element is a substance that cannot be broken down into other substances by chemical reactions.
- There are 92 naturally occurring elements.
- Each element has a unique symbol, usually the first one or two letters of the name. Some of the symbols are derived from Latin or German names.
A compound is a substance consisting of two or more elements in a fixed ratio.
Table salt (sodium chloride or NaCl) is a compound with equal numbers of atoms of the elements chlorine and sodium.
While pure sodium is a metal and chlorine is a gas, they combine to form an edible compound. This change in characteristics when elements combine to form a compound is an example of an emergent property.

25 chemical elements are essential to life.

About 25 of the 92 natural elements are known to be essential for life.
- Four elements—carbon (C), oxygen (O), hydrogen (H), and nitrogen (N)—make up 96% of living matter.
- Most of the remaining 4% of an organism’s weight consists of phosphorus (P), sulfur (S), calcium (Ca), and potassium (K).
Trace elements are required by an organism but only in minute quantities.
- Some trace elements, like iron (Fe), are required by all organisms.
- Other trace elements are required by only some species.
- For example, a daily intake of 0.15 milligrams of iodine is required for normal activity of the human thyroid gland.

Concept 2.2 An element’s properties depend on the structure of its atoms

Each element consists of unique atoms.
An atom is the smallest unit of matter that still retains the properties of an element.
- Atoms are composed of even smaller parts, called subatomic particles.
- Two of these, neutrons and protons, are packed together to form a dense core, the atomic nucleus, at the center of an atom.
- Electrons can be visualized as forming a cloud of negative charge around the nucleus.
Each electron has one unit of negative charge.
Each proton has one unit of positive charge.
Neutrons are electrically neutral.
The attractions between the positive charges in the nucleus and the negative charges of the electrons keep the electrons in the vicinity of the nucleus.
A neutron and a proton are almost identical in mass, about 1.7 × 10?24 gram per particle.
For convenience, a smaller unit of measure, the dalton, is used to measure the mass of subatomic particles, atoms, or molecules.
The mass of a neutron or a proton is close to 1 dalton.
The mass of an electron is about 1/2000 that of a neutron or proton.
Therefore, we typically ignore the contribution of electrons when determining the total mass of an atom.
All atoms of a particular element have the same number of protons in their nuclei.
- This number of protons is the element’s unique atomic number.
- The atomic number is written as a subscript before the symbol for the element. For example, 2He means that an atom of helium has 2 protons in its nucleus.
Unless otherwise indicated, atoms have equal numbers of protons and electrons and, therefore, no net charge.
- Therefore, the atomic number tells us the number of protons and the number of electrons that are found in a neutral atom of a specific element.
The mass number is the sum of the number of protons and neutrons in the nucleus of an atom.
- Therefore, we can determine the number of neutrons in an atom by subtracting the number of protons (the atomic number) from the mass number.
- The mass number is written as a superscript before an element’s symbol (for example, 4He).
The atomic weight of an atom, a measure of its mass, can be approximated by the mass number.
- For example, 4He has a mass number of 4 and an estimated atomic weight of 4 daltons. More precisely, its atomic weight is 4.003 daltons.
While all atoms of a given element have the same number of protons, they may differ in the number of neutrons.
Two atoms of the same element that differ in the number of neutrons are called isotopes.
In nature, an element occurs as a mixture of isotopes.
- For example, 99% of carbon atoms have 6 neutrons (12C).
- Most of the remaining 1% of carbon atoms have 7 neutrons (13C) while the rarest carbon isotope, with 8 neutrons, is 14C.
Most isotopes are stable; they do not tend to lose particles.
- Both 12C and 13C are stable isotopes.
The nuclei of some isotopes are unstable and decay spontaneously, emitting particles and energy.
- 14C is one of these unstable isotopes, or radioactive isotopes.
- When 14C decays, one of its neutrons is converted to a proton and an electron.
- This converts 14C to 14N, transforming the atom to a different element.
Radioactive isotopes have many applications in biological research.
- Radioactive decay rates can be used to date fossils.
- Radioactive isotopes can be used to trace atoms through metabolic processes.
Radioactive isotopes are also used to diagnose medical disorders.
- For example, a known quantity of a substance labeled with a radioactive isotope can be injected into the blood, and its rate of excretion in the urine can be measured.
- Also, radioactive tracers can be used with imaging instruments to monitor chemical processes in the body.
While useful in research and medicine, the energy emitted in radioactive decay is hazardous to life.
- This energy can destroy molecules within living cells.
- The severity of damage depends on the type and amount of radiation that the organism absorbs.

Electron configuration influences the chemical behavior of an atom.

Simplified models of the atom greatly distort the atom’s relative dimensions.
To gain an accurate perspective of the relative proportions of an atom, if the nucleus was the size of a golf ball, the electrons would be moving about 1 kilometer from the nucleus.
- Atoms are mostly empty space.
When two elements interact during a chemical reaction, it is actually their electrons that are involved.
The nuclei do not come close enough to interact.
The electrons of an atom vary in the amount of energy they possess.
Energy is the ability to do work.
Potential energy is the energy that matter stores because of its position or location.
- Water stored behind a dam has potential energy that can be used to do work turning electric generators.
- Because potential energy has been expended, the water stores less energy at the bottom of the dam than it did in the reservoir.
Electrons have potential energy because of their position relative to the nucleus.
- The negatively charged electrons are attracted to the positively charged nucleus.
- The farther electrons are from the nucleus, the more potential energy they have.
Changes in an electron’s potential energy can only occur in steps of a fixed amount, moving the electron to a fixed location relative to the nucleus.
- An electron cannot exist between these fixed locations.
The different states of potential energy that the electrons of an atom can have are called energy levels or electron shells.
- The first shell, closest to the nucleus, has the lowest potential energy.
- Electrons in outer shells have more potential energy.
- Electrons can change their position only if they absorb or release a quantity of energy that matches the difference in potential energy between the two levels.
The chemical behavior of an atom is determined by its electron configuration—the distribution of electrons in its electron shells.
- The first 18 elements, including those most important in biological processes, can be arranged in 8 columns and 3 rows.
- Elements in the same row fill the same shells with electrons.
- Moving from left to right, each element adds one electron (and proton) from the element before.
The first electron shell can hold only 2 electrons.
- The two electrons of helium fill the first shell.
Atoms with more than two electrons must place the extra electrons in higher shells.
- For example, lithium, with three electrons, has two in the first shell and one in the second shell.
The second shell can hold up to 8 electrons.
- Neon, with 10 total electrons, has two in the first shell and eight in the second, filling both shells.
The chemical behavior of an atom depends mostly on the number of electrons in its outermost shell, the valence shell.
- Electrons in the valence shell are known as valence electrons.
- Lithium has one valence electron; neon has eight.
Atoms with the same number of valence electrons have similar chemical behaviors.
An atom with a completed valence shell, like neon, is nonreactive.
All other atoms are chemically reactive because they have incomplete valence shells.
The paths of electrons are often portrayed as concentric paths, like planets orbiting the sun.
In reality, an electron occupies a more complex three-dimensional space, an orbital.
The orbital represents the space in which the electron is found 90% of the time.
- Each orbital can hold a maximum of two electrons.
- The first shell has room for a single spherical 1s orbital for its pair of electrons.
- The second shell can pack pairs of electrons into a spherical 2s orbital and three dumbbell-shaped 2p orbitals.
The reactivity of atoms arises from the presence of unpaired electrons in one or more orbitals of their valence shells.
- Electrons occupy separate orbitals within the valence shell until forced to share orbitals.
- The four valence electrons of carbon each occupy separate orbitals, but the five valence electrons of nitrogen are distributed into three unshared orbitals and one shared orbital.
When atoms interact to complete their valence shells, it is the unpaired electrons that are involved.