Lectures 2-3: Atoms, Ions, and Molecules
Greek or Latin roots:
- hydro: water
- hyper: excessive, high
- hypo: deficient, below
- phobos: fear, horror
- philos: love
Key Terms:
- Matter
- Element
- Periodic table
- Atom
- Neutron
- Proton
- Electron
- Atomic nucleus
- Octet rule
- Ion
- Cation
- Anion
- Ionic compound
- Ionic bond
- Molecule
- Covalent bond (single, double, triple;
nonpolar or polar)
- Electronegativity
- Nonpolar molecule
- Polar molecule
- Amphipathic molecule
- Intermolecular attractions
- Hydrogen bond
- Hydrophobic interactions
- Solvent
- Solute
- Hydrophilic
- Hydrophobic
- Acid
- Base
- pH
- Neutralization
- Buffer
Learning objectives:
- Define matter, and list its 3 forms
- Describe and differentiate among the subatomic particles that compose atoms
- Describe how elements are organized in the periodic table based on the number
of electrons in the outer shell
- State the octet rule
- Define an ion
- List some common ions in the body
- Differentiate between cations and anions
- Describe how charges are assigned to ions
- Define an ionic bond
- List some examples of ionic compounds
- Describe a covalent bond and explain its formation based on the octet rule
- List the four most common elements in the human body
- Distinguish between single, double, and triple covalent bonds
- Describe the difference between a nonpolar molecule, polar, and amphipathic
molecules
- Describe hydrogen bonding between polar molecules
- List and define the intermolecular attractions between nonpolar molecules
- List the functions of water in the human body
- List the different properties of water and provide and example of the importance of
each property within the body
- Distinguish between electrolytes and nonelectrolytes
- Describe the chemical interactions between polar substances and water
- Explain how amphipathic molecules interact in water to form chemical barriers,
such as the plasma membrane
- Describe what is formed when water dissociates
- Explain the difference between an acid and a base
- Define pH and explain the relative pH values of both acids and bases
- Explain the term neutralization, and describe how the neutralization of both an
acid and a base occur
- Describe the action of a buffer
To fully understand how the body functions, we need to know some basic chemistry:
what atoms, ions, and molecules look like, and how they interact with each other to
carry out vital life processes
I. ATOMS & ELEMENTS
A. ATOMS & ELEMENTS IN THE HUMAN BODY
Atoms are the building blocks of ____________: any substance that has mass
and takes up space
Three forms of matter in the human body: solids (like bone),
liquids (like blood), and gases (like oxygen)
An atom occurs neutrally in nature as an ____________: a
substance made entirely from one type atom
Elements are unique — they cannot be
chemically converted into something else or
broken down into different atoms.
Elements have physical and chemical
properties that are organized into chart form
in the ___________________:
Note that elements
and atoms have the
same name; i.e.,
“hydrogen” can mean
either a hydrogen
atom, or hydrogen the
element. However, a
hydrogen atom is just
one atom of
hydrogen, whereas
hydrogen the element
is two atoms of
hydrogen, because
most elements
require more than 1
atom to be stable
(more on this in a bit)
92 elements
92 elements in nature… but only a few elements are common in the human body:
B. ATOMIC STRUCTURE
1. Atoms are made of three subatomic particles, distinguished by mass and
charge:
• ____________: subatomic particle with no charge and a mass of 1 amu
• ____________: subatomic particle with positive charge (+1) and a mass of
1 amu
• ____________: subatomic particle with negative
charge (-1) and negligible mass
amu = atomic mass unit
(1.66 x 10-27 kg)
2. Subatomic particles are organized like a “mini solar system”:
• Protons and neutrons are located in the core (center) of the atom, in the
_________________
• Electrons circle around the nucleus in
__________ (AKA: orbitals, clouds)
- Innermost shell can hold up to 2 electrons
- All other shells can hold up to 8 electrons
(some exceptions)
- Electrons fill inner shells first
3. Atoms are neutral (# of protons = # of electrons) but not necessarily stable
— atoms are most stable when their outer shell is full (i.e., with 2 electrons
for H and He, and 8 electrons for all other elements) →
______________: elements tend to lose, gain, or share electrons to obtain
complete outer shells with eight electrons. This explains how atoms
interact with each other and form compounds or molecules.
Clinical applications
——————————————————-——————————
= extra credit on
exams!
•
•
•
•
CLINICAL APPLICATION: Radioisotopes
Atoms are neutral (# of protons = # of electrons),
but often differ in the number of neutrons to form
isotopes: different atoms of the same element that
have the same number of protons and electrons
but differ in the number of neutrons —> similar
properties, different masses
Radioisotopes are isotopes that are unstable b/c
they have too many neutrons, so they get rid of
neutrons until stable
Neutrons are released in the form of radiation,
which can be detected by medical imaging devices
Radioisotopes can thus be introduced to the human
body, where they are used by specific organs to
help visualize those organs
——————————————————-——————————
Thyroid
gland
II. IONS, IONIC COMPOUNDS, & IONIC BONDS: electrons transferred
A. An _____ forms when electrons are transferred between atoms
1. ___________: ion that loses electron(s) and acquires
a positive charge
2. ___________: ion that gains electron(s) and acquires
a negative charge
Will an atom form a cation or an anion? That depends on the number of
electrons in the outer shell.
Recall that atoms differ in their number of subatomic particles. As you move from
left to right on the periodic table, the number of electrons in the outermost shell
(valence shell) increases by 1:
+1
+2
+3
Atoms with one, two, or three
electrons in the outer shell generally
donate electrons and become ______
-3
-2
Atoms with four
electrons in the outer
shell generally share
electrons and form
molecules held
together by covalent
bonds
-1
Atoms with eight
electrons in the
outer shell do not
combine with
other elements
— they are the
chemically inert
noble gases
Atoms with five, six, or seven
electrons in the outer shell
generally gain electrons and
become _________
Cations and anions bind together
to form ionic compounds held
together by ionic bonds
B. Opposites attract! Positively charged cations and negatively charged anions
may attach to each other like “magnets”, forming an
___________________: alternating arrangement of
cation(s) and anion(s)
which is held together by
___________________: “magnetic” attractions between
positive and negative charges
Ionic compounds are also
known as salts
(ex: NaCl) and function as
electrolytes: substances that
when dissolved in water
dissociate into cations and
ions that can conduct an
electric current
III. MOLECULES & COVALENT BONDS: electrons shared
Rather than transferring electrons, atoms may instead achieve chemical stability by
sharing electrons
Note: some texts distinguish
A. A ___________________ forms when electron(s) are
shared between atoms;
Increasing stability
this sharing of electrons binds atoms together through
___________________
• _______________________: 1 pair of
shared electrons
• _______________________: 2 pairs of
shared electrons
• _______________________: 3 pairs of
shared electrons
The greater the # of shared electrons,
the stronger (more stable) the bond
Elements that commonly form covalent
bonds in the body: “HONC”
• Hydrogen (H): 1 bond
• Oxygen (O): 2 bonds
• Nitrogen (N): 3 bonds
• Carbon (C): 4 bonds
between molecular
compounds (different atoms
bonded together) and
molecules (same or different
atoms bonded together); we
will stick with “molecule”
B. NONPOLAR vs POLAR COVALENT BONDS & MOLECULES
Atoms may not share electrons equally… how electrons are shared is determined
by each atom’s ____________________: the relative attraction for electrons
More electronegative atoms “hog” electrons
1. _________________________ form when atoms have
similar electronegativities and share electrons equally
Occur between atoms of the same element (ex: O2), or
between C and H
_______________________ contain mostly nonpolar covalent bonds formed
between the same element, by C—H bonds, or both
2. _________________________ form when atoms have different
electronegativities and share electrons unequally
Occur between atoms of different elements — more
electronegative atom hogs electrons and develops a
partial negative charge (𝛿-), less electronegative atom
develops a partial positive charge (𝛿+)
Electronegativity increases
from left to right
(increasing # of protons
pulling on electrons) and
bottom to top (electrons in
shells closer to the
nucleus)
_______________________ contain mostly polar
covalent bonds formed between different elements (ex:
O—H, C—O)
Exception: molecules with polar covalent bonds
extending in opposite directions can be nonpolar
because the partial charges cancel each other out
(no longer acts like a magnet w/ 1 (+) and 1 (-) end)
3. _______________________ are large molecules with nonpolar and polar
parts
C. INTERMOLECULAR ATTRACTIONS
In addition to covalent bonds between the atoms within a molecule, molecules
sometimes have weak chemical attractions to other molecules, called
intermolecular attractions:
1. ___________________: weak attraction
between a partially positive hydrogen atom
within one polar molecule and a partially
negative atom within another polar molecule
(usually O, or N)
Collectively can be strong!
2. ___________________: result when nonpolar
molecules are placed in water or another polar
substance
Though weak, intermolecular attractions play an important role in the 3D shape
of complex “macromolecules” (ex: DNA and proteins) (Lecture 4)
SUMMARY:
IV. Special detour: Water (b/c it makes up 2/3 of the human body!)
Water (H2O) occurs mainly in liquid form in the human body.
Liquid water has many functions:
• Transports substances (nutrients, O2, waste, etc.) (via blood, lymph, urine)
• Lubricates (e.g., serous fluid)
• Cushions (e.g., cerebrospinal fluid)
• Regulates body temperature
• Buffers pH
These functions depend on 2 characteristics of water:
1. Water forms many ______________________, which:
• Make water _________ — water molecules stick to each other and to
other substances
• Help regulate __________________________ —
because energy is required to break H bonds before
temperature change
Sweat
absorbs
body heat →
cooling
2. Water is the ________________________ (most substances
dissolve in it)
a) ____________________ (“water loving”)
substances dissolve in water: polar
molecules and ions (anything with a charge)
•
Polar molecules remain intact (form H
bonds with a “shell” of water molecules)
•
Electrolytes (ionic compounds or acids and
bases) dissociate into ions (which then form
H bonds with a “shell” of water molecules)
Ions are charged —> can conduct
electrical currents!
_________: a substance (water) that has the ability to dissolve other substances
_________: a substance (e.g., sugar, salt) that dissolves in water
b) ____________________ (“water fearing”)
substances do not dissolve in water:
nonpolar molecules
Polar water molecules exclude (force out)
nonpolar molecules and minimize the
contact between polar and nonpolar
c) ________________________ partially
dissolve in water — polar portion dissolves,
nonpolar portion is repelled
Form important chemical barriers, such as
the plasma membrane: polar portions face
towards the water and nonpolar portions
face away from the water, resulting in
bilayers or micelles
ACIDS & BASES: a special type of hydrophilic substance
1. Water spontaneously dissociates into hydronium (H3O+) and hydroxide (OH-)
ions:
H2O + H2O → H3O+ + OHsimplified to
H2O → H+ + OH_______: any substance that dissociates in water to produce both a H+ and an
anion — a H+ donor
acid in water → H+ + anion (increases amount of H+ in solution)
Strong acids dissociate more and donate more H+
_______: any substance that accepts H+ when added to a solution — a
H+ acceptor
base in water + H+ → base—H+ (decreases amount of H+ in solution)
Strong bases accept more H+
2. ____ (= -log[H+]): measure of the relative amounts of H+ ions in a solution
• Water is neutral and has a pH of 7 ([H+]=10-7)
• Acidic solutions (acid + water) have _____ [H+] and _____ pH (0 to <7)
• Basic solutions (base + water) have _____ [H+] and _____ pH (>7 to 14)
Inverse relationship between [H+] and pH: as [H+] increases, pH decreases, and vice versa
Changing by 1 pH unit represents a 10-fold change in [H+]; 2 pH units = 100-fold, 3 = 1000…
Why is this important? In acidic solutions with high [H+], H+ can bind to other
substances and disrupt their structure (ex: HCl in the stomach denatures proteins for
digestion); in basic solutions with low [H+], H+ may be “pulled” from other substances
and disrupt their structure. So, acids and bases are carefully maintained!
3. __________________ occurs when a solution that is either acidic or
basic is returned to neutral (pH 7)
• Add base to neutralize an acidic solution
(ex: pancreatic “juice” and Tums)
small
intestine
stomach
pancreas
• Add acid to neutralize a basic solution
4. _________: a substance that helps prevent pH changes if excess acid or
excess base is added — accepts H+ from excess acid or donates H+ to excess
base
• Carbonic acid (H2CO3) and bicarbonate (HCO3-) help maintain normal
blood pH (7.35-7.45)