Summary Biol 105 Test 1 Study Guide

Test 1 Study Guide

Ch 2: Small Molecules and the Chemistry of Life
- neutron: particle with no electric charge that may be found inside nucleus
- electron: negatively charged particle that surrounds nucleus
o less mass than a proton; approx. 0.0005 Da and can usually be ignored
o determines how atoms will combine with other atoms to form stable
associations
- proton: positively charged particle inside of nucleus
o Dalton: standard unit of measurement for the mass of a proton; single proton or
neutron has a mass of 1 dalton (Da) = 1.7 x 10-24 grams
- atom: tiny, electrically charged particle that forms matter; has volume and mass
o nucleus: dense, positively charged center of an atom
o generally, are electrically neutral; number of electrons = number of protons
- molecule: chemical substance composed of 2 or more atoms joined by covalent or ionic
bonds
- element: fundamental substance that contains only one kind of atom; atoms of each
element have characteristics that distinguish them from the atoms of other elements
o physical / chemical properties depend on number of particles in the atom
o isotope: differing forms of the same element; same number of protons in the
nuclei but different numbers of electrons
- orbital: region of space surrounding atomic nucleus where electron is found 90% of the
time; have characteristic shapes and orientations
o a given orbital can be occupied by a maximum of 2 electrons; any atom larger
than helium must have electrons in 2 or more orbitals
o filled in specific sequences in a series of electron shells – first shell (innermost, 1
orbital), second shell (4 orbitals, 8 electrons), additional shells (elements with
more than 10 electrons have 3+ electron shells)
o s orbital: spherical orbital contained by every electron shell
o p-orbital: dumbbell shaped orbital in the 2nd and subsequent shells
- covalent bond: chemical bond that forms when 2 atoms attain stable electron numbers
in their outermost shells by sharing 1 or more pairs of electrons
o each atom contributes one member of each electron pair
o strong, stable, and length/angle of each bond, with respect to other bonds, is
always the same for a given pair of elements
o shapes can change; long chains of atoms can rotate freely to alter structures to
fit other molecules
 shapes of molecules contribute to biological functions
o multiple covalent bonds can occur
 bond energies are higher
- electronegativity: tendency of an atom to attract electrons when it occurs as part of a
compound; attractive force an atomic nucleus exerts on electrons

, o depends on how many positive charges it has (atoms with more protons = more
positive = more attractive to electrons)
o depends on distance between nucleus and electron in outer valence shell; closer
the electrons are, the higher the electronegative pull
o fluorine is most electronegative, followed by oxygen (3.5); many organisms
exploit the electronegativity of oxygen (moving electrons between C and O atoms
powers living systems)
- polarity: refers to a molecule with separate and opposite electric charges at 2 ends
(poles)
o molecules are termed “polar” if they contain polar covalent bonds and if one
region is more polar than others; water is most prevalent example
o nonpolar covalent bonds: covalent bond between atoms that have equal sharing
of electrons; happens 2 atoms are close to one another in electronegativity
o polar covalent bonds: electrons are drawn to 1 nucleus more than the other,
resulting in unequal distribution of charge; typically happens when 2 atoms differ
in electronegativity by more than 0.4
o partial charges that result from polar covalent bonds produce polar molecules or
polar regions of large molecules, which influence interactions that those
molecules have with other polar molecules
- ionic bonds: form as a result of electrical attraction between ions bearing opposite
charges; electrostatic attraction between positively and negatively charged ions
o ions: electrically charged particles that form when at atom gains / loses 1 or
more electrons; usually stable and no more electrons are gained / lost
o can form bonds that result in stable compounds; in solids, the attractions are
stronger because ions are close together
o less strong than covalent bonds; can interact with polar molecules
 salt dissolving in water
o cation: ion with 1 or more positive charges
 Na+, Ca2+, H+, Mg2+, K+
o anion: negatively charged ion
 Cl-
- hydrogen bonds: weak electrostatic bond which arises from attraction between slight
positive charge on a hydrogen atom and a slight negative charge on a nearby oxygen or
nitrogen atom
o not restricted to water molecules; can form between electronegative atoms in
one molecule and hydrogen atoms involved in polar covalent bonds in another /
the same molecule
o weaker than most ionic bonds due to partial charges; have strength in numbers
and can influence structure / properties of a substance
o heat will break hydrogen bonds and 3d structure of molecule will change
- hydrophobic interactions: bring together nonpolar molecules in the presence of a polar
substance (especially water); in water, these molecules aggregate with one another
rather than the water molecules and create weak chemical interactions between

, themselves; can form weak interactions with water, but those interactions are weaker
than the hydrogen bonds between water molecules
o hydrophilic: having an affinity for water; hydrophobic / nonpolar molecules are
more likely to associate with one another than water
o polar molecules can interact with other polar molecules through weak
attractions of hydrogen bonds (or interact with water = hydrophilic)
- van der Waals forces: weak attractions between atoms in close proximity, resulting from
the interaction of the electrons of one atom with the nucleus of another; this type of
attraction is about a fourth as strong as a hydrogen bond
o result from random variations in electron distribution in 1 molecule, which can
create opposite charge distributions in the adjacent molecule & a weak,
temporary positive or negative attraction
o occur in nonpolar and polar molecules
 in nonpolar molecules, they can induce cohesion between molecules that
do not form ionic bonds or hydrogen bonds
o brief, weak but collectively can create substantial attraction
- chemical reaction: change in the composition or distribution of atoms of a substance,
with consequent alterations in properties
o occurs when moving atoms collide with sufficient energy to combine or change
bonding partners
- energy: capacity to do work or move matter against an opposing force
o capacity to accomplish change in physical and chemical systems
o chemical reactions do not create or destroy energy, but create changes in the
form of energy
- acid: release H+ in solution
o contain carboxyl group –COOH
o incomplete reaction = weak acid; ionization of weak acids in water is somewhat
reversible
o acids that fully ionize in solution are strong acids (HCl, H2SO4 sulfuric acid);
ionization of strong acids in water is virtually irreversible
o lower pH; solution with pH value of less than 7 is acidic and contains more H+
ions than OH- ions
- base: accept H+
o weak bases include bicarbonate ion (HCO3-), which can accept an H+ ion and
become carbonic acid (H2CO3), and ammonia (NH3), which can accept H+ and
become an ammonium ion (NH4+); ionization of weak bases is somewhat
reversible
o NaOH is a strong base; ionization of strong bases in water is virtually irreversible
o biological compounds that contain –NH2 (the amino group) are also bases; it
accepts H+
o water is a weak acid and a weak base
o solution with a pH value above 7 is basic