Download 1 LS 1a Glossary Fall 2014 This glossary is meant to clarify some of

LS 1a Glossary
Fall 2014
This glossary is meant to clarify some of the terms that you may hear in lecture, section, or during office
hours during the semester. Many of these terms you do not need to know but they may prove useful in
your studies. If there are additional terms you would like to see added or if you continue to be confused
by a term, please email us at [email protected].
Amino Acid: An amino acid is a molecule that has a central alpha carbon (“Cα”) that is bound to: a) an
amine group; b) a carboxylic acid group; c) a hydrogen atom; and d) a side chain that varies from one
amino acid to the next. Amino acids are the monomer units that comprise proteins. Naturally occurring
proteins are generally constructed from a pool of 20 amino acids.
Covalent Bond: A covalent bond describes a bond between two atoms in which electrons are shared
between the two atoms. Bonds between atoms with electronegativity differences of less than 1.7 are said
to be covalent. Covalent bonds can be either nonpolar, in which case the electrons are evenly shared
between the two atoms, or polar, in which case the electrons spend more time around one atom than the
other.
Dipole: A dipole can be either a bond or a molecule that is positively-charged at one end and negativelycharged at the other end. The positive and negative charges can be either full or partial.
Dispersion Force: See “Van der Waals Interactions.”
DNA: Deoxyribonucleic acid (DNA) is a biological polymer whose primary role is the storage of genetic
information. DNA is a nucleic acid, and as such, it is a polymer comprised of nucleotide monomers. The
nucleobases found in DNA include adenine, guanine, cytosine, and thymine.
Electron: An electron is a subatomic particle that is negatively-charged. Electrons carry an electrical
charge that is exactly opposite to the charge of a proton, but electrons are only a tiny fraction of the
mass of a proton. Nearly all chemistry is based on the movement and rearrangement of electrons within
atoms and molecules.
Electron Shell: The electrons surrounding an atomic nucleus are grouped into shells, like the layers of
an onion, according to the energy the electrons possess. An electron shell is a grouping of electrons with
similar energies, and atoms can use several different shells to accommodate electrons of different
energies. Shells nearest the nucleus have the lowest energy and electron shells further away have higher
energies. Each electron shell can only hold a certain number of electrons (shell 1 holds 2 electrons, shell
2 holds 8 electrons, etc.). As a result, shells nearer to the nucleus are filled first before electrons are
added to higher level shells. An example of a neutral atom lithium having three electrons is shown below:
the first two electrons occupy the most-inner first shell and the third occupies the outer second shell.
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Electronegativity: Electronegativity is the tendency of an atom to attract electrons. Atoms with greater
electronegativity will tend to pull the electrons in a bond closer to itself, giving it a partially-negative
charge and leaving the other atom to which it is bonded with a partially-positive charge. Atoms with
greater electronegativies can also more stably sustain a full negative charge (e.g., oxygen or chlorine).
Electrolyte: “Electrolyte” is effectively another word for “salt.” An electrolyte is a molecule that dissolves
into ions when placed in water, such as sodium chloride.
Formal Charge: Formal charge is a convention used to express whether an atom in a molecule “owns”
more or less electrons than what is required for the atom to be neutral (given its number of protons).
Formal charge is calculated by subtracting the number of non-bonded (“lone pair”) electrons and half the
number of electrons involved in bonds from the number of valence electrons found in the free neutral
atom. The convention used to calculate formal charge assumes electrons in bonds are always shared
evenly; therefore, atoms that have a neutral formal charge may still have a partial charge if they are part
of a polar bond.
Full Charge: A full charge is a term used to describe an amount of charge corresponding to the charge
of either an electron (if negative) or a proton (if positive).
Functional Group: A functional group is a portion within a larger molecule that conveys properties
and/or reactivities to the molecule.
Hydrogen Bond: A hydrogen bond is a unique type of dipole-dipole interaction because it has a
directional component. Hydrogen bonds can form between a partially-negatively charged “acceptor” atom
(usually F, O, or N) and a partially-positively charged “donor” hydrogen atom, which itself is covalently
bonded to a second electronegative atom. There are several conditions that must be met for hydrogen
bonds to form: 1) the partially negative F, O, or N (the “acceptor” atom) must have a lone pair of
electrons; and 2) the partially-positive “donor” hydrogen atom and acceptor atom must be appropriately
oriented relative to one another. Hydrogen bonds have an ideal bond angle of 180°.
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Induced-Dipole Interaction: See “Van der Waals Interactions.”
Intermolecular Interaction: An intermolecular interaction is an electrostatic attraction that occurs
between different molecules or between far-away portions of the same molecule. Intermolecular
interactions vary in strength depending upon the magnitudes of the charges involved and the distances
over which they act.
Ion: An ion is any atom or molecule that contains a full net charge because of having more electrons
than protons, or vice versa.
Ionic Bond: An ionic bond is a bond between a positively-charged ion (a “cation”) and a negativelycharged ion (an “anion”). A cation has fewer electrons than protons; an anion has more electrons than
protons. Ionic bonds can form between two atoms in which the electronegativity difference between the
two atoms is so great (> 1.7) that one atom effectively loses its electron to the more electronegative
atom.
Lewis “dot” structure: A Lewis “dot” structure is a style of diagram that represents the arrangement of
atoms and valence electrons within a molecule. Lewis dot structures show the location of all atoms and
valence electrons. Valence electrons are shown either as lone pairs or as forming bonds: single bonds are
shown as pairs of valence electrons shared between two atoms; double bonds are shown as four
electrons shared between two atoms; triple bonds are shown as six electrons shared between two atoms.
A valid Lewis dot structure satisfies the octet rule for each atom. An example of a Lewis dot structure of
carbon dioxide (CO2) is shown below:
Lewis structure: A Lewis structure is similar to a Lewis “dot” structure, with the lone difference being
that pairs of electrons between atoms representing covalent bonds are replaced with lines. An example of
a Lewis structure of carbon dioxide (CO2) is shown below:
Macromolecule: A macromolecule is a large molecule of high relative molecular mass. Such molecules
tend to be polymers whose structures are comprised of repeated units derived from molecules of low
relative molecular mass. Proteins, nucleic acids, and many types of carbohydrates are examples of
macromolecules.
Monomer: A monomer is a small-molecule building block that can be used to construct a larger polymer:
polymers are the result of iteratively attaching monomers together. Nucleotides and amino acids are
examples of biological monomers that comprise nucleic acids and proteins, respectively.
Nucleic Acid: Nucleic acids are a class of biological polymer that includes DNA and RNA. They are called
“nucleic” because they were first discovered in the cell nucleus, and “acid” because they contain an acidic
phosphoryl group.
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Nucleotide: Nucleotides are molecules that contain a sugar (either ribose or deoxyribose), a nucleobase,
and phosphate group(s) attached to the sugar’s 5’ carbon. The term nucleotide is also used to refer to
the monomers that comprise nucleic acids. For example, deoxyadenosine monophosphate and
deoxyadenosine triphosphate are both nucleotides.
Nucleus (Atomic): The nucleus, in the context of an atom, is the central portion of the atom that
contains both neutrons (neutrally-charged subatomic particles) and protons (positively-charged subatomic
particles).
Octet Rule: The octet rule describes the tendency of atoms to form bonds such that their valence shells
of electrons are filled with eight electrons. This rule applies particularly to elements such as C, N, O, and
F, which are in the second row of the periodic table. Sulfur and phosphorus do not always follow this
rule, a phenomenon we call “octet expansion.” Hydrogen (in the first row of the periodic table) is most
stable when it can fill its valence shell with two electrons.
Orbital: An orbital is a probabilistic description of where an electron can mostly likely be located at any
given time. Each orbital holds two electrons. Orbitals form various three-dimensional shapes; s orbitals
are essentially spherical, and p orbitals form a two-lobed shape. The electronic configuration of orbitals is
beyond the scope of this course, so no need to worry about it.
Partial Charge: A partial charge refers to any amount of charge density that is greater than zero but
less than the charge of a proton (if positive) or an electron (if negative). Partial charges are indicated
with a lower-case Greek letter “delta” with a superscript + or – indicating the polarity of the charge (e.g.,
δ+ represents a partial-positive charge).
Polar Bond: A polar bond is a type of covalent bond in which electrons are unevenly shared between
the two atoms in the bond. Bonds connecting atoms that have electronegativity differences greater 0.4
but less than 1.7 are polar covalent bonds. These bonds form an electrical dipole due to the uneven
distribution of electrons, and as a result, the more electronegative of the two atoms in the bond tends to
be partially-negatively charged while the less electronegative atom tends to be partially-positively
charged.
Polymer: A polymer is a macromolecule that is comprised of many repeating units (a.k.a. monomers).
Nucleic acids, proteins, and some carbohydrates are examples of biological polymers.
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Protein: A protein is a macromolecular biological polymer derived from individual monomers called
amino acids. Proteins assume a wide variety of folded shapes that perform varied cellular functions.
RNA: Ribonucleic acid (RNA) is a biological polymer that plays roles in a variety of cellular roles, such as
gene expression, gene coding, and enzymatic catalysis. RNA is a nucleic acid, and as such, it is comprised
of nucleotide monomers. The nucleobases found in RNA include adenine, guanine, cytosine, and uracil.
Salt Bridge: Another name for an ionic bond.
Small Molecule: A small molecule is a molecule of low molecular mass (generally less than 100 atoms).
Such molecules tend to be highly diverse relative to macromolecules, which tend to be comprised of
repeating subunits.
Standard Line Drawing: A standard line drawing is a style of diagram that represents the arrangement
of atoms and bonds within a molecule. By convention, the end point of a line or the vertex between two
or more lines in a standard line drawing is assumed to be a carbon atom. Each assumed carbon atom is
assumed to be bounded to an appropriate number of hydrogen atoms such that its octet is fill (e.g., if a
carbon is at the end point of a line, it would need to be bound to three hydrogen atoms in order to have
a full octet). All atoms other than carbon and hydrogen must be shown explicitly on a standard line
drawing. All hydrogen atoms that are bound to non-carbon atoms must also be shown explicitly. Lone
pair electrons do not have to be shown, but they are sometimes shown for clarity. It is like a Lewis
structure, but without explicitly labeling the carbons and the lone pairs of electrons. An example of a
standard line drawing is shown below on the left. To the right is the same molecule with all atoms
labeled.
Lewis structure
Equivalent standard line drawing
Valence Electron: A valence electron refers to an electron located in the outer-most electron shell of an
atom. These electrons are nearly always the electrons that are involved in chemical reactions.
Van der Waals Interaction/Force (VDW): Van der Waals interactions or van der Waals forces are
weak electrostatic intermolecular interactions that occur due to transient, instantaneous dipoles that form
within atoms and/or molecules in response to their proximity to other atoms/molecules. A transient dipole
in one molecule can transiently induce a dipole in a neighboring molecule. These “transient” or
“instantaneous” dipoles are due to the random motion of electrons within atoms or bonds which leads to
short-lived areas of positive and negative charge (dipoles). These short-lived charges are electrostatically
attractive, allowing non-polar molecules to weakly attract one another. These transient dipoles can also
be induced by the presence of a charge (in the form of an ion, a partially charged atom, or even another
instantaneous dipole); this occurs because the charge triggers the motion of electrons via either
attraction or repulsion, leading to polarization in the molecule/atom being affected. Van der Waals
interactions are generally weak, but their strength increases proportionally to the surface area over which
they can form; extended molecules with extensive surface area form more significant van der Waals
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interactions than more compact molecules. These interactions are also called “induced-dipole:induceddipole interactions,” “van der Waals” interactions, or “London Dispersion Forces.”
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