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.

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