Chapter 2: The Molecules of Life
2.1 Properties of Atoms
● Elements- a small number of fundamental substances combined in various ways
which make up the materials of nature.
● 118 elements are known. 94 occur naturally and 24 have been created artificially.
● Atom- the basic unit of matter.
○ Contains a dense central nucleus made up of:
■ Protons- positively charged particles.
■ Neutrons- electrically charged particles.
○ Electron- negatively charged particles, moves around the nucleus at
some distance from it.
● Protons + neutrons = atomic mass, the mass of the atom.
● Each proton and neutron has a mass of 1, whereas an electron has negligible
mass.
● Isotopes are atoms of the same element that have different numbers of
neutrons.
● Typically, an atom has the same number of protons and electrons.
● Electrically charged atoms are called ions.
○ An atom that has lost an electron is positively charged.
○ An atom that has gained an electron is negatively charged.
● Orbital- where an electron is present most of the time.
○ The maximum number of electrons in any orbital is two.
○ Electrons in orbitals close to the nucleus have less energy than electrons
in orbitals farther away, so electrons fill up orbitals close to the nucleus
before occupying those farther away.
○ Several orbitals can exist at a given energy level, or shell.
● The periodic table of the elements- elements are arranged by increasing
number of protons, the atomic number. The elements in a column share similar
chemical properties.
2.2 Molecules and Chemical Bonds
● Atoms can combine with other atoms to form molecules, which are groups of
two or more atoms attached together that act as a single unit.
● When two atoms form a molecule, the individual atoms interact through what is
called a chemical bond, a form of attraction between atoms that holds them
together.
● The ability of atoms to combine with other atoms is determined by the electrons
farthest from the nucleus, valence electrons, they are at the highest energy
level.
● When the outermost orbitals of two atoms come into proximity, two atomic
orbitals each containing one electron merge into a single orbital containing a full
, complement of two electrons. The merged orbital is called a molecular orbital,
and each shared pair of electrons constitutes a covalent bond that holds the
atoms together.
● Two adjacent atoms can sometimes share two pairs of electrons, forming a
double bond.
● Molecules are most stable when the two atoms forming a bond share enough
electrons to completely occupy the outermost energy level or shell.
● The unequal sharing of electrons results from a difference in the ability of the
atoms to attract electrons, electronegativity.
● Electronegativity increases across a row in the periodic table; as the number of
protons across a row increases, electrons are held more tightly to the nucleus.
● A polar covalent bond forms when electrons are shared unequally between two
atoms.
● A covalent bond between atoms that have the same electronegativity is a
nonpolar covalent bond, the atoms share the bonding electron pair almost
equally.
● When an atom of very high electronegativity is paired with an atom of very low
electronegativity, the difference in electronegativity is so great that the
electronegative atom “steals” the electron from its less electronegative partner.
○ The two ions are not covalently bound, but because opposite charges
attract they associate with each other in an ionic bond.
● Chemical reaction- a process by which atoms or molecules, called reactants,
are transformed into different molecules, called products.
○ During a chemical reaction, atoms keep their identity but change which
atoms they are bonded to.
2.3 Water: The Medium of Life
● Aqueous- watery.
● Water molecules have polar covalent bonds and an uneven distribution of
electrons.
● A molecule that has regions of positive and negative charge is called a polar
molecule.
○ Molecules are classified by how they interact with water:
■ Hydrophilic compounds- polar, they dissolve readily in water
● Water is a good solvent, capable of dissolving many
substances.
■ Hydrophobic compounds- nonpolar.
● Hydrophobic effect- polar molecules like water exclude
nonpolar ones, drives such biological processes as the
folding of proteins and the formation of cell membranes.
2.1 Properties of Atoms
● Elements- a small number of fundamental substances combined in various ways
which make up the materials of nature.
● 118 elements are known. 94 occur naturally and 24 have been created artificially.
● Atom- the basic unit of matter.
○ Contains a dense central nucleus made up of:
■ Protons- positively charged particles.
■ Neutrons- electrically charged particles.
○ Electron- negatively charged particles, moves around the nucleus at
some distance from it.
● Protons + neutrons = atomic mass, the mass of the atom.
● Each proton and neutron has a mass of 1, whereas an electron has negligible
mass.
● Isotopes are atoms of the same element that have different numbers of
neutrons.
● Typically, an atom has the same number of protons and electrons.
● Electrically charged atoms are called ions.
○ An atom that has lost an electron is positively charged.
○ An atom that has gained an electron is negatively charged.
● Orbital- where an electron is present most of the time.
○ The maximum number of electrons in any orbital is two.
○ Electrons in orbitals close to the nucleus have less energy than electrons
in orbitals farther away, so electrons fill up orbitals close to the nucleus
before occupying those farther away.
○ Several orbitals can exist at a given energy level, or shell.
● The periodic table of the elements- elements are arranged by increasing
number of protons, the atomic number. The elements in a column share similar
chemical properties.
2.2 Molecules and Chemical Bonds
● Atoms can combine with other atoms to form molecules, which are groups of
two or more atoms attached together that act as a single unit.
● When two atoms form a molecule, the individual atoms interact through what is
called a chemical bond, a form of attraction between atoms that holds them
together.
● The ability of atoms to combine with other atoms is determined by the electrons
farthest from the nucleus, valence electrons, they are at the highest energy
level.
● When the outermost orbitals of two atoms come into proximity, two atomic
orbitals each containing one electron merge into a single orbital containing a full
, complement of two electrons. The merged orbital is called a molecular orbital,
and each shared pair of electrons constitutes a covalent bond that holds the
atoms together.
● Two adjacent atoms can sometimes share two pairs of electrons, forming a
double bond.
● Molecules are most stable when the two atoms forming a bond share enough
electrons to completely occupy the outermost energy level or shell.
● The unequal sharing of electrons results from a difference in the ability of the
atoms to attract electrons, electronegativity.
● Electronegativity increases across a row in the periodic table; as the number of
protons across a row increases, electrons are held more tightly to the nucleus.
● A polar covalent bond forms when electrons are shared unequally between two
atoms.
● A covalent bond between atoms that have the same electronegativity is a
nonpolar covalent bond, the atoms share the bonding electron pair almost
equally.
● When an atom of very high electronegativity is paired with an atom of very low
electronegativity, the difference in electronegativity is so great that the
electronegative atom “steals” the electron from its less electronegative partner.
○ The two ions are not covalently bound, but because opposite charges
attract they associate with each other in an ionic bond.
● Chemical reaction- a process by which atoms or molecules, called reactants,
are transformed into different molecules, called products.
○ During a chemical reaction, atoms keep their identity but change which
atoms they are bonded to.
2.3 Water: The Medium of Life
● Aqueous- watery.
● Water molecules have polar covalent bonds and an uneven distribution of
electrons.
● A molecule that has regions of positive and negative charge is called a polar
molecule.
○ Molecules are classified by how they interact with water:
■ Hydrophilic compounds- polar, they dissolve readily in water
● Water is a good solvent, capable of dissolving many
substances.
■ Hydrophobic compounds- nonpolar.
● Hydrophobic effect- polar molecules like water exclude
nonpolar ones, drives such biological processes as the
folding of proteins and the formation of cell membranes.
