Basic Chemistry and Major
Biomolecules
• Atoms
• Chemical Bonds & Interactions
• Acids & Bases (pH defined)
• Major Biomolecules
– Lipids
–Polysacharides
– Nucleic Acids
– Proteins
Atomic Structure
How do atoms interact to
form molecules?
• Covalent Bonds (atoms share electrons)
• Electrostatic Interactions (opposites attract):
– Ionic Bonds (full charges)
– Polar Bonds (partial charges; Hydrogen Bonds)
• Hydrophobic Interactions
(“water haters stick together”)
Covalent bonds (true bonds): electrons are shared between
outer orbitals of atoms so to make pairs. One shared pair is a single bond;
two shared pairs is a double bond; three shared pairs is a triple bond.
Ionic Bonds (strong electrostatic attraction): Atoms with
extra electrons are negatively charged (called anion). Atoms with fewer
electrons are positively charged (called cations). These ions of opposite
charge attract to form salts. Salts dissolve in water because individual
cations and anions become dissociated by the water molecules.
Na has only one
e- in its outer
orbital; that e- is
easily donated,
or lost; the result
is a net positive
charge.
Cl has a nearly
complete outer orbital; it
strongly accepts
another e-; the result is
a net negative charge.
Polar Bonds (weak electrostatic attractions): Some
molecules have atoms covalently bound together, but one atom may pull
the shared pair of electrons more toward its nucleus. This creates partial
charges across the molecule (one side partly negative and the other side
partly positively charged); this type of molecule is said to be polar.
Partial positives and partial negatives of two polar molecules can attract
each other. Water is a good example.
Not just water molecules
can form H-bonds!
Hydrophobic Interactions (nonpolar aggregation):
Nonpolar compounds include
the hydrocarbons like oils.
They are insoluble in water.
It is more energetically
favorable for nonpolar
compounds to aggregate
together in water than stay
apart.
Place two drops of vegetable
oil in a bowl of water, and with
some time they will collide
and become one. The
warmer the water the faster
this happens. Why?
Cell membranes form from
lipids due to hydrophobic
interactions.
Water as a Strong Solvent:
Waters small size and
polarity makes it a very
powerful dissolving agent
(solvent) for many
compounds (solute) when
they are added to water,
particularly salts and polar
solutes, like sugar. Notice
how multiple water
molecules surround the
ions by charge – partial
charge attractions.
Acids and
Bases
Water, like a salt, can become
dissociated into a proton (H+) and a
hydroxyl ion (OH-). In pure water
there is an equal balance of protons
and hydroxyl ions. We refer to the
solution as neutral (pH = 7).
Acids are compounds that add protons
(H+) to water. Extra protons make a
solution acidic (pH < 7).
Bases are compounds that add a
hydroxyl ion to water. Extra hydroxyl
ions makes the solution basic, or
alkaline (pH > 7).
pH = -log [H+]
Lipids:
They are a class of hydrocarbons; nonpolar compounds or possess a
nonpolar portion; major constituent of storage fat and cell membranes;
hydrocarbon many be saturated or unsaturated (refers to hydrogens
bound to carbons); longer saturated hydrocarbons are rigid, or solidify at
warmer temperatures.
A dehydration reaction (water’s released).
Fat is a glycerol (yellow) with three
fatty acids bound to it by ester
linkages; 3 waters released to form.
Sterols are another class of lipid;
cholesterol is a sterol.
Amphipathic (polar and nonpolar sides)
membrane lipids:
Lipid Bilayer Membrane: polar end
toward outside water (hydrophilic);
nonpolar hydrocarbons (hydrophobic)
to interior of membrane.
Polysaccharides:
Polymers of monosaccharide building blocks (simple sugars; carbohydrates).
Bind together by a glycosidic bond via dehydration synthesis.
Two monosaccharides binding makes a disaccharide.
Structural Polymer
Storage Polymer
Nucleic Acids
Nucleotides are the
building blocks of nucleic
acids made of a nitrogen
base, pentose (5C) sugar,
and phosphate(s).
RNA has ribose sugar;
ribonucleic acids.
DNA has deoxyribose
sugar; deoxynucleic acids.
Double stranded.
Nucleotide Precursors
Purines:
Missing
hydroxyl
oxygen on
carbon 2’ of
pentose.
T in DNA;
no U.
U replaces
T in RNA.
Pyrimidines:
UMP
Nucleotides
They may have one, two, or three
phosophate groups. (e.g. UMP vs ATP)
Phosphates bind together by phosphoanhydride bonds; very high energy; ATP
is the common storage molecule for
chemical energy in the cell.
Nucleic Acids polymerize
by adding the 5’
phosphate end of a new
nucleotide triphosphate to
the 3’ hydroxyl; energy
and a pyrophosphate (PP)
are released to form a new
phosphodiester bond.
5’
ATP
3’
DNA stand base pairs complement.
Amino Acids and Peptide Bonds
The building
blocks of
polypeptides.
Twenty different
amino acids whose
occurrence in a
polypeptide is
genetically coded
in the DNA.
Ribosome enzymes
form peptide bonds.
Polypeptide(s) folds into a protein.
Always three levels of structure, but some have four.
Metabolic Reactions & Enzymes
* Metabolism refers to the many chemical reactions used by a cell to both breakdown organic molecules for release of new energy (catabolism) and build up new
molecules for growth, which uses energy (anabolism).
* Metabolic reactions can proceed very fast reaction rates due to the involvement
of enzymes as reaction catalysts (some reactions would take forever without a
catalyst).
* Some reactions occur spontaneously (without add energy); in fact, these so
called exergonic reaction release energy.
* Some reactions require added energy if they are going to happen at all. The
extra energy comes from involving ATP, which releases energy as itself reacts to
ADP and Pi. These are called endergonic reactions.
* Some reactions neither require nor release much energy. They’re reversible.
* Three major types of reactions:
Synthesis
Decomposition
Exchange
Reaction Progress
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