Section
3: Chemical Building Blocks of Life
I.
What are atoms?
II.
The Covalent Bond
III.
The Noncovalent Bond
IV.
Chemical Reactions
V.
What are the chemical building
blocks of life?
I.
Atoms
v Everything
in the natural world is made up of 92 natural chemical elements.
o
Each element is indicated by a one
or two letter symbol.
o
Elements are organized on the
periodic table.
v One
unit of a particular element is an atom.
o
An atom is the smallest unit of an
element that still has the characteristic chemical properties of that element.
o
Atoms (and therefore elements)
differ from each other based on the different combinations of three atomic
components.
§ Two
components are electrically charged: Protons (positive) and Electrons
(negative).
§ One
lacks an electrical charge: Neutrons (neutral),
o
A single atom has a dense central
core called the nucleus that contains one or more protons, and is thus
positively charged.
§ With
the exception of hydrogen atoms, the nucleus also contains one or more
neutrons.
§ The
nucleus is surrounded by one or more negatively charged electrons.
§ The
positively charged nucleus and negatively charged electrons balance out such
that atoms are electrically neutral.
·
However, the number of electrons
is not fixed. An atom can gain from,
lose to, and share with electrons from other atoms.
·
An atom that has become charged
due to a loss or gain of electrons is called an ion.
v Chemical
compounds are formed when atoms of one element form linkages with each other or
with atoms of other elements.
o
The smallest unit of a compound is
a molecule.
o
Molecular formulas represent
compounds made up of molecules ranging in size from two atoms to many thousands
of atoms.
v The
atomic number distinguishes an atom from other atoms. This is the number of protons (and thus
electrons) in an atom.
v The
atomic mass is the sum of an atom’s protons and neutrons. (These are not always equal.)
v Some
elements can contain different numbers of neutrons. These variants of elements are called
isotopes.
o
Ex: radioisotope carbon-14
II.
The covalent bond
v The
strongest type of linkage that can hold atoms together to form molecules is the
covalent bond, which link atoms within a single molecule.
v Number
of possible covalent bonds between atoms depends on number of electrons needed
to fill its outer shell.
v Examples:
water (H20) and methane (CH4)
III.
The noncovalent bond
v Noncovalent
bonds are the most common linkages between separate molecules and between
different parts of a single large molecule.
v Noncovalent
bonds are far weaker than covalent bonds, but their strength lies in numbers.
v Noncovalent
bonds do not involve atom sharing.
v Hydrogen
bonds are noncovalent.
o
Form due to slightly different
electrical charges that exist between polar molecules.
o
Ex: hydrogen bond between water
molecules because of slight positive hydrogen charge in Hydrogen and slight
negative charge in Oxygen
o
Water molecules can form hydrogen
bonds with other polar compounds, which results in these compounds dissolving
in water.
§ Compounds
that can dissolve in water are known as soluble.
§ A
solution is any combination of a solute (a dissolved substance) and a solvent (the liquid, usually water,
into which it has dissolved).
v Ionic
bonds are noncovalent.
o
An ionic bond relies on the
“opposites attract” principle, but one atom completely loses an electron in its
outer shell to another atom’s outer shell.
o
Ex: NaCl
o
The strength of the bonds differs
when the molecules are dry or surrounded by water.
IV. Chemical
Reactions
v Processes
that break and form bonds between atoms are known as chemical reactions.
v The
following is an example of standard notation for chemical reactions.
o
3H2 + N2 à 2NH3
o
Atoms on left of arrow are
reactants: atoms on right are products.
v All
chemical reactions rearrange atoms, but a chemical reaction can neither create
nor destroy atoms.
v Some
of the most important chemical reactions to life are those that occur in water,
particularly those involving two classes of compounds: acids and bases.
o
Acid: polar compound that
dissolves in water and loses one or
more hydrogen ions (H+).
o
Base: polar compound that accepts hydrogen ions from surroundings,
leaving hydroxide (OH-) behind.
o
Acids and bases interact with
water molecules in different ways and have opposite effects on the amount of
free hydrogen ions in water.
§ The
concentration of free hydrogen ions in water influences the chemical reactions
of many other molecules and is expressed as a scale of numbers (pH scale) from
0 to 14, where 0 represents the highest concentration of free hydrogen ions and
14 represents the lowest.
§ When
water has no contains no acids or bases, the concentrations of free hydrogen
ions and hydroxide ions are equal, and the pH is said to be neutral.
§ Below
7 is considered acidic, and above 7 is basic.
o
Buffers prevent large changes in
pH.
V.
Chemical Building Blocks of Life
v There
are four major classes of compounds in living organisms: Carbohydrates, Nucleic
Acids, Proteins, and Fats. These all consist of different arrangements of
carbon atoms associated with hydrogen.
Oxygen, nitrogen, phosphorus, and sulfur may also be present. (CHNOPS)
o
Carbon is the predominant element
in living systems
§ Can
form large molecules that contain thousands of atoms
§ One
carbon atom can form strong covalent bonds with four other atoms.
§ Carbon
can bond to carbon, forming long chains, branched molecules, or even rings.
§ All
carbon compounds found in nature are referred to as organic molecules.
§ Most
carbon compounds contain about 20 atoms and can combine with other molecules of
about the same size to form larger structures called macromolecules.
·
Monomers (approximately 70) are
put together to form polymers (nearly infinite types)
·
Functional groups
are groups of covalently bonded atoms that have the same specific chemical
properties of whatever molecule they are part of. Some help establish covalent
linkages between monomers by providing molecules with sites that can react with
other molecules
o
Ex: Amino groups, Carboxyl groups,
Hydroxyl groups, Phosphate groups
v Carbohydrates
o
Monosaccharides are the monomers
that join to form di- and polysaccharides.
o
Monosaccharides are made up of
units containing carbon, hydrogen, and oxygen atoms in the ratio of 1:2:1 or
(CH2O)n,
with n ranging from 3 to 7.
§ Ex:
5-carbon sugar: (CH2O)5 or C5H10O5
o
Best known example of a
monosaccharide is glucose.
§ Maltose
= dimer of glucose
§ Cellulose
and Starch = polymers of glucose
v Nucleic
Acids
o
Nucleotides are the monomers that
make up genetic material in all organisms and act as energy “currency” in
cells.
o
Each nucleotide is made up of a
nitrogen base covalently bonded to a 5-carbon sugar that is covalently bonded
to a phosphate group (1 phosphate + 4 oxygen atoms).
o
Two kinds of nucleic acids (DNA
and RNA) are distinguished from each other by the sugar in their nucleotide and
the nitrogen bases that bond with that sugar.
§ 5
nitrogen bases: adenine, guanine, cytosine, thymine (DNA), uracil (RNA)
o
Nucleotides can also assist in
energy transfer
§ ATP
(adenosine triphosphate): adenine + ribose + 3 phosphate groups
v Proteins
o
Amino acids are the monomers used
to build proteins.
§ 20
different amino acids, each with an “alpha carbon” attached to a hydrogen atom,
an amino group, a carboxyl group, and an R group.
o
A protein’s sequence of amino
acids is known as the primary structure.
§ The
next level of organization is the secondary structure: amino acids that have
been folded into spirals (alpha helixes) or sheets (beta pleated sheets).
§ The
third level of organization is tertiary structure, which is an additional
folding of a protein sequence.
§ Some
proteins require an additional level of organization, the quaternary structure,
which includes groups of closely associated protein sequences.
o
Changes in amino acid sequence can
cause the protein to function improperly.
§ Ex:
Sickle Cell Anemia
§ Denaturation
can also cause the protein to function improperly.
·
This occurs when bonds holding
protein shape in place are broken.
§ Improper
Protein folding can cause adverse affects brought on by particular diseases.
v Lipids
o
Fatty acids are the key components
of lipids. Fatty acids are composed
primarily of long hydrocarbon chains ending with a carboxyl group.
§ Chains
consist of 16 or 18 carbon atoms that can vary in the way they are covalently
bonded together.
·
Saturated: fatty acids in which
all the carbon atoms are linked together by single
covalent bonds (and bonded to a full complement of hydrogen atoms).
·
Unsaturated: when one or more of
the carbon atoms are linked together by double
covalent bonds (not a full complement of hydrogen atoms)
o
Lipids are a large group of
molecules that include a wide variety of molecules, the unifying principle
being that they are insoluble in water.
§ Some
have one end soluble in water and the other not.
o
Fats (triglycerides) are types of
lipids composed of three fatty acids combined with a simple three-carbon
molecule called glycerol.
o
Phospholipids: two fatty acid
chains and a negatively charged phosphate group to glycerol.
§ Phospholipid
bilayers are the basis of all cell membranes, which are essential physical
structures for living organisms.
o
Steroids: 4-carbon ring
structure. Each type of steroid differs
from others by the groups of atoms attached to these rings.
§ Ex:
cholesterol, testosterone, estrogen