Essential Chemistry
Studying Life from The Chemical Level
• Biology is a multidisciplinary science
• Biology includes the study of life at many levels
• Living organisms are subject to basic laws of physics and
chemistry
• We will take the reductionist approach. We will start at
the atomic level and work our way up to the level of cell
activity
• Cells consist of enormous numbers of chemicals that give
the cell the properties we recognize as life
Matter: Elements and Compounds
• Organisms are composed of matter
• Matter is anything that takes up space and has mass
• Matter is found on the Earth in three physical states
– Solid
– Liquid
– Gas
• Matter is composed of chemical elements
– Elements are substances that cannot be broken down into
other substances
– There are 92 naturally occurring elements on Earth
Elements and Compounds
• An atom is the smallest unit of matter that still retains the
properties of an element, it cannot be broken down to other
substances by chemical reactions
• Each element consists of one kind of unique atom
• A compound is a substance consisting of two or more elements
in a fixed ratio
Sodium
Chlorine
Sodium chloride
Essential Elements of Life
• About 25 of the 92 elements are essential to life
• Carbon, hydrogen, oxygen, and nitrogen make up
96% of living matter
• Most of the remaining 4% consists of calcium,
phosphorus, potassium, and sulfur
• Trace elements are those required by an organism in
minute quantities
Elements Essential to Life
– Four of these
make up about
96% of the
weight of the
human body
– Trace elements
occur in smaller
amounts
Figure 2.3
Essential Elements of Life
SPONCH
Subatomic Particles
•
Atoms are composed of subatomic particles
•
Relevant subatomic particles include:
– Neutrons (no electrical charge)
– Protons (positive charge)
– Electrons (negative charge)
•
Neutrons and protons form the atomic nucleus
•
Electrons form a cloud around the nucleus
Nucleus
(a)
(b)
Cloud of negative
charge (2 electrons)
2
Protons
2
Neutrons
2
Electrons
Atomic Number and Atomic Mass
• Atoms of the various elements differ in number of
subatomic particles
• An element’s atomic number is the number of protons
• The number of protons (atomic number) determines the
element’s properties
• An element’s mass number is the sum of protons plus
neutrons in the nucleus
• Atomic mass, the atom’s total mass, can be approximated by
the mass number
Periodic Chart
Atomic number
Element symbol
Mass number
Isotopes
• Atoms of an element have the same number of protons but may differ in
number of neutrons
• Isotopes are two atoms of an element that differ in number of neutrons
• Most isotopes are stable, but some are radioactive, giving off particles
and energy
• Some applications of radioactive isotopes in biological research:
– Tracing atoms through metabolic processes
– Diagnosing medical disorders
Energy Levels of Electrons
• Energy is the capacity to cause change
• Potential energy is the energy that matter has because of its location or
structure
• The electrons of an atom differ in their amounts of potential energy
• An electron’s state of potential energy is called its energy level, or electron
shell
Third energy level (shell)
A ball bouncing down a flight
of stairs provides an analogy for
energy levels of electrons.
Second energy level (shell)
Energy
absorbed
First energy level (shell)
Energy
lost
Atomic
nucleus
Electron Configuration and Chemical Properties
• The chemical behavior of an atom is determined by the distribution of
electrons in electron shells
• The periodic table of the elements shows the electron distribution for
each element
Hydrogen
1H
2
Atomic number
He
Atomic mass
First
shell
4.00
Helium
2He
Element symbol
Electron-shell
diagram
Lithium
3Li
Beryllium
4Be
Boron
5B
Carbon
6C
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Sodium
11Na
Magnesium
12Mg
Aluminum
12Al
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Third
shell
Electron Orbitals
• An orbital is the three-dimensional space where an electron
is found 90% of the time
• Each electron shell consists of a specific number of orbitals
Electron
orbitals
y
x
z
1s orbital
2s orbital
Three 2p orbitals
1s, 2s, and 2p orbitals
Electron-shell
diagrams
First shell
(maximum
2 electrons)
Second shell
(maximum
8 electrons)
Neon, with two
filled shells
(10 electrons)
Electron Shell Significance
• Each Orbital holds a maximum of 2 electrons each
• Several orbitals may be the same distance from the nucleus and
thus contain electrons of the same energy
• Such electrons are said to occupy the same energy level or shell
• The chemical behavior of an atom is mostly determined by the
valence electrons
• Valence electrons are those in the outermost shell, or valence shell
First
electron shell
(can hold
2 electrons)
Outermost
electron shell
(can hold
8 electrons)
Electron
Hydrogen (H)
Atomic number = 1
Carbon (C)
Atomic number = 6
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8
Valence and Chemical Reactions
• Atoms with incomplete valence shells can share or
transfer valence electrons with certain other atoms
• Atoms “desire” full outer orbitals
– Give up electrons (Na)
– Take electrons (Cl)
– Share electrons (O2)
• Rule of Eights for filling each shell
• Noble gases - full outer shells (inert)
Chemical Reactions
• Cells constantly rearrange molecules by breaking existing chemical bonds and
forming new ones
• Such changes in the chemical composition of matter are called chemical
reactions
• Chemical reactions enable atoms to give up or acquire electrons in order to
complete their outer shells
– These interactions usually result in atoms staying close together
– The atoms are held together by chemical bonds
Hydrogen gas Oxygen gas
Water
Reactants
Products
Chemical Reactions
• Are dependent on :
– Concentration
– Speed
– Energy (energy of activation)
– Orientation
Types of Chemical Reactions
• Synthesis reactions - atoms or molecules combine to
form a product
• Decomposition reactions - molecules breakdown into
smaller molecules or atoms
• Exchange reactions - molecules exchange constituent
components (swap partners)
• Reversible reactions - the product of a previous
reaction can revert to the original reactants.
Chemical Products
• Element: a substance composed of only one type of atom
(all the atoms have the same number of protons).
• Molecule: a unit composed of two or more atoms joined
together by chemical bonds
• Compound: a substance composed of 2 or more elements
that have been joined by chemical bonds
• Mixture: a combination of 2 or more substances that do
NOT chemically bond e.g. sugar mixed with salt
Periodic Chart
Ionic Bonds
•
Atoms sometimes strip electrons from their bonding partners
•
An example is the transfer of an electron from sodium to chlorine
•
After the transfer of an electron, both atoms have charges
•
A charged atom (or molecule) is called an ion
•
–
An anion is a negatively charged ion
–
A cation is a positively charged ion
An ionic bond is an attraction between an anion and a cation - oppositely
charged ions
Ionic Compounds
• Compounds formed by ionic bonds are called
ionic compounds, or salts
• Salts, such as sodium chloride (table salt), are
often found in nature as crystals
Na+
Cl–
Periodic Chart
Covalent Bonds
• Molecules are formed by covalent bonds
Hydrogen atoms (2 H)
• A covalent bond is when two atoms share
one or more pairs of outer-shell electrons
(valence electrons)
• In a covalent bond, the shared electrons
count as part of each atom’s valence shell
• Much stronger than ionic bonds – holds lots
of Energy
• A single covalent bond, or single bond, is
the sharing of one pair of valence electrons
• A double covalent bond, or double bond, is
the sharing of two pairs of valence electrons
• Covalent bonds can form between atoms of
the same element or atoms of different
elements
Hydrogen
molecule (H2)
Covalent Bonds
Name
(molecular
formula)
Oxygen (O2)
Electronshell
diagram
Structural
formula
Spacefilling
model
Covalent Bonds
Name
(molecular
formula)
Electronshell
diagram
Structural
formula
Spacefilling
model
Water (H2O)
Name
(molecular
formula)
Methane (CH4)
Electronshell
diagram
Structural
formula
Spacefilling
model
Covalent Bonds
Figure 2.9
Electronegativity
• Outer orbital (valence shell) determines reactivity of atom Electronegativity
• Electronegativity is an atom’s attraction for the electrons in a covalent
bond
• The more electronegative an atom, the more strongly it pulls shared
electrons toward itself
–
O
+
H
H
H2O
+
Polar Covalent Bond
• In a nonpolar covalent bond, the atoms share the
electron equally
• In a polar covalent bond, one atom is more
electronegative, and the atoms do not share the
electron equally
The Structure of Water
– Its two hydrogen atoms are joined to one oxygen atom by
single covalent bonds
– But the electrons of the covalent bonds are not shared equally
between oxygen and hydrogen
– This unequal sharing makes water a polar molecule
()
()
()
()
Unnumbered Figure 2.2
Hydrogen Bonds
• A hydrogen bond forms
when a hydrogen atom
covalently bonded to one
electronegative atom is also
attracted to another
electronegative atom
()
Hydrogen bond
()
()
• In living cells, the
electronegative partners are
usually oxygen or nitrogen
atoms
()
()
()
()
()
(b)
Figure 2.11b
Hydrogen Bonds
–
+
Water
(H2O)
+
Hydrogen bond
–
Ammonia
(NH3)
+
+
+
Van der Waals Interactions
• Molecules or atoms that are very close
together can be attracted by fleeting charge
differences
• These weak attractions are called van der
Waals interactions
• Collectively, such interactions can be strong
Weak Chemical Bonds
• Most of the strongest bonds in organisms are
covalent bonds that form a cell’s molecules
• Weak chemical bonds, such as ionic bonds and
hydrogen bonds, are also important
• Weak chemical bonds reinforce shapes of large
molecules and help molecules adhere to each
other
Biological Importance
• Acts as a powerful solvent
• Participates in chemical reactions
• Water has a high specific heat which moderates temperature - absorbs
and releases heat very slowly, minimizes temperature fluctuations to
within limits that permit life
– Heat is absorbed when hydrogen bonds break
– Heat is released when hydrogen bonds form
• Requires a great amount of heat to change to a gas
– Heat of vaporization - the quantity of heat a liquid must absorb for 1
gram of it to be converted from a liquid to a gas
– Evaporative cooling - Allows water to cool a surface due to water’s high
heat of vaporization
• Acts as a lubricant
Polarity & Hydrogen Bonds
• Cohesion - molecules attract other
water molecules
• Capillarity
– Water molecules are drawn up a narrow
tube
– Helps pull water up through the
microscopic vessels of plants
• Surface tension
– water molecules on the surface cling to
each other – related to cohesion
– Is a measure of how hard it is to break
the surface of a liquid
• Adhesion - water molecules attract
other charged substances
Water as a Solvent
• Water is a versatile solvent due to its polarity
• It can form aqueous solutions
• The different regions of the polar water molecule can interact with
ionic compounds called solutes and dissolve them
Negative
oxygen regions
of polar water molecules
are attracted to sodium
cations (Na+).
–
Na
+
+
–
Positive
hydrogen regions
of water molecules
cling to chloride anions
(Cl–).
–
Na
+
Cl–
+
Cl –
–
+
+
–
–
+
+
–
–
+
+
–
–
Acids, Bases, and pH
• Dissociation of water molecules leads to acidic and basic
conditions that affect living organisms
– Water dissociates into hydronium ions and hydroxide ions
– Changes in the concentration of these ions can have a great
affect on living organisms
–
+
H
H
H
H
H
H
H
Hydronium
ion (H3O+)
+
H
Hydroxide
ion (OH–)
Acids, Bases, and pH
• Acid - A chemical compound that dissociates into
one or more hydrogen ions (H+) and one or more
negative ions (anions). An acid donates H+ ions
(protons) to solutions
• Base - Dissociates into one or more positive ions
(cations) and one or more hydroxide ions (OH-). A
base accepts H+ ions and removes them from
solution, reducing the hydrogen ion concentration
of a solution
pH
• To describe the acidity of a
solution, we use the pH scale
• Is a measure of the concentration
of H+ ions in a solution
Oven cleaner
Household bleach
Household ammonia
Basic
solution
• Is determined by the relative
concentrations of H+
– Basic = High pH = few
many OH-
Milk of magnesia
Seawater
Human blood
Pure water
H +,
Neutral
solution
– Acidic = Low pH = many H+,
few OH-
Urine
Tomato juice
Grapefruit juice
Acidic
solution
Lemon juice;
gastric juice
pH scale
Figure 2.17
pH Scale
• The pH scale is a logarithmic scale
used to express the amount of H+
ions in a solution.
• pH is defined as the negative log of
the [H+] of a solution
• A change of one whole number
represents a tenfold (10X) change in
the number of H+ ions.
• A solution with pH 3 has ten times
as many H+ ions as a solution with
pH 4
Buffers
•
A buffer is a substance that helps minimize the change in the pH of a
solution when acids or bases are added.
•
Consist of an acid-base pair that reversibly combines with hydrogen
ions
•
Buffers work by releasing H+ when their concentration falls, and
absorbing H+ when their concentration rises.
•
Buffers are important to living organisms because most cells can survive
and function normally only within a relatively narrow range
1
-
pH
14
[H+]