Chemical Foundations for Cells
- Atomic Physics
- Matter: anything that occupies space and has mass.
- Is highly condensed packages of energy (E=Mc2)
- It includes solids, liquids, and gases and plasma.
- Ordinary matter is made of some 92 naturally occurring elements
- The "organic" elements include N, O, C, H, S and P.
- Structure of Atoms
- An atom is the smallest unit of matter that retains the
properties of a particular element.
- Atoms are composed of three primary subatomic particles:
- Protons (p+) are part of the atomic nucleus and have a positive charge.
- Neutrons are also a part of the nucleus; they are neutral.
- Electrons (e-) have a negative charge. They "move around the
- The atomic number is defined as the number of
protons in the nucleus.
- The atomic mass of an atom is equal to the number of
protons plus the number of neutrons.
- IsotopesVariant Forms of Atoms
- Atoms with the same number of protons (for example, carbon with six) but a different
number of neutrons (carbon can have six, seven, or eight) are called isotopes
(C12, C13, C14).
- Some radioisotopes are unstable and tend to decay
into more stable atoms.
- They can be used to date rocks and fossils.
- Some can be used as tracers to follow the path of an atom in a series of reactions or to
- The Nature of Chemical Bonds
- Electrons and Energy Levels
- Electrons are attracted to protons but are repelled by other electrons.
- Orbitals permit electrons to stay as close to the nucleus and as far from
each other as possible.
- Each orbital contains one or two electrons.
- Orbitals can be thought of as occupying shells around the nucleus.
- Atoms with "unfilled" orbitals in their outermost shell tend to be reactive with other atoms.
- Electrons and the Bonding Behavior of Atoms
- A chemical bond is a union between atoms formed when
they give up, gain, or share electrons.
- Whether one atom will bond with another depends on the number and arrangement of its
- From Atoms to Molecules
- A molecule is a bonded unit of two or more (same or
- Compounds are substances in which two or more different elements are combined
in fixed proportions.
- A mixture contains two or more elements in
intermingled proportions that can vary.
- Important Bonds in Biological Molecules
- Ion Formation and Ionic Bonding
- When an atom loses or gains one or more electrons, it becomes positively or negatively
charged: an ion.
- In an ionic bond, (+) and (-) ions are linked by
mutual attraction of opposite charges, for example, NaCl.
- Covalent Bonding
- A covalent bond holds together two atoms that share
one or more pairs of electrons.
- In a nonpolar covalent bond, atoms share electrons
- In a polar covalent bond, because atoms share the
electron unequally, there is slight difference in charge between the two poles of the
bond; water is an example.
- Hydrogen Bonding
- In a hydrogen bond, an atom or a molecule interacts
weakly with a hydrogen atom already taking part in a polar covalent bond.
- These bonds impart structure to liquid water and stabilize nucleic acids and other large
- Properties of Water
- Polarity of the Water Molecule
- Because of the electron arrangements in the water molecule, a polarity results that
allows water to form hydrogen bonds with one another and other polar substances.
- Polar substances are hydrophilic (water loving);
nonpolar ones are hydrophobic (water dreading) and are
repelled by water.
- Waters Temperature-Stabilizing Effects
- Water tends to stabilize temperature because it can
absorb considerable heat before its temperature changes.
- This is an important property in evaporative and freezing processes.
- Waters Cohesion and Adhesion
- Hydrogen bonding of water molecules provides cohesion
(capacity to resist rupturing).
- Cohesion imparts surface tension and helps pull water through plants for example.
- Adhesion is when water sticks to itself. It is demonstrated when water beads
up on top of wax.
- Cohesion and adhesion together cause the capillary effect.
- Waters Solvent Properties
- Water is a great solvent because ions and polar molecules (solutes) dissolve in it.
- The solvent properties of water are greatest with
respect to polar molecules because "spheres of hydration" are formed around the
- Acids, Bases, and Buffers
- The pH Scale
- pH is a measure of the H+ concentration in a solution; the greater the H+
the lower the pH scale.
- The scale extends from 0 (acidic) to 7 (neutral) to 14 (basic).
- The interior of living cells is near pH = 7.
- Acids and Bases
- A substance that releases hydrogen ions (H+) in solution is an acid;
for example, HCl.
- Substances that release ions such as OH- (hydroxide ions) that can combine with hydrogen
ions are called bases.
- Buffers Against Shifts in pH
- A buffer system is a partnership between a weak acid
and the base that forms when it dissolves in water.
- Buffer molecules combine with, or release, H+ to prevent drastic changes in pH.
- Carbonic acid is one of the bodys major buffers.
- A salt is an ionic compound formed when an acid reacts with a base; example: NaOH + HCl
> NaCl + H2O.
- Many salts dissolve into ions that serve key functions in cells; nerve function, for
example, is dependent on ions of sodium, potassium, and calcium.