Biochemistry Basics
Section 1.1
Subatomic Particles and the Atom
• Protons (+ charge) and
neutrons (neutral)
– found in the nucleus
• Electrons (- charge)
– Surround the nucleus in a
“cloud” or orbital
• Orbital
– the 3D space where an
electron is found 90% of the
time
– Each orbital can fit only 2
electrons
Bonding – Covalent Bonds
Hydrogen atoms (2 H)
• Atoms bond 1 In each hydrogen
atom, the single electron
through is held in its orbital by
its attraction to the
+ +
interaction of their proton in the nucleus.
valence (outer
orbital) electrons 2 When two hydrogen
atoms approach each
• Covalent bond
other, the electron of
each atom is also + +
attracted to the proton
– electrons are in the other nucleus.
shared between The two electrons
3
atoms and the become shared in a
covalent bond,
valence orbitals forming an H2 + +
overlap molecule.
Hydrogen
molecule (H2)
Name Electron- Structural Space-
(molecular shell formula filling
formula) diagram model
Water (H2O).
Two hydrogen
atoms and one O H
oxygen atom are
joined by covalent H
bonds to produce a
molecule of water.
Methane (CH4).
Four hydrogen
atoms can satisfy H
the valence of
one carbon
atom, forming H C H
methane.
H
Ionic Bonds
• In some cases, atoms strip electrons away
from their bonding partners
• Ionic bond – electrons are transferred from
one atom to the other, resulting in a negative
ion (anion) and a positive ion (cation), which
are electrostatically attracted to each other
The lone valence electron of a sodium Each resulting ion has a completed
atom is transferred to join the 7 valence valence shell. An ionic bond can form
electrons of a chlorine atom. between the oppositely charged ions.
+ –
Na Cl Na Cl
Na+ Cl–
Na Cl Sodium on Chloride ion
Sodium atom Chlorine atom (a cation) (an anion)
(an uncharged (an uncharged
atom) atom) Sodium chloride (NaCl)
• Covalent bonds are stronger than ionic bonds
• Covalent and Ionic bonds are intramolecular
forces of attraction because they are within
molecules
Polarity
• Electronegativity
– Is the attraction of an atom
for electrons
• The more electronegative
an atom
– The more strongly it pulls
electrons toward itself
• The smaller the atom
– the more electronegative
• to determine the type of bond between two atoms, calculate the
difference between their electronegativity values
=0 covalent strong electrons
shared equally
electrons
0 < x < 1.7 polar covalent partially shared
>= 1.7 ionic weak electrons not
(extreme polarity) shared
• the greater their difference in electronegativity, the greater the
polarity of that substance
• Polar Covalent Bond – electrons are shared unequally between
atoms of different electronegativity; electrons are closer to the
atom with the higher value
Because oxygen (O) is more electronegative than hydrogen (H),
shared electrons are pulled more toward oxygen.
This results in a
– partial negative
charge on the
oxygen and a
O partial positive
charge on
the hydrogens.
H H
+ +
H2O
Intermolecular Forces
• intermolecular forces of attraction exist
between molecules
• London forces
– form when the electrons of one molecule are
attracted to the positive nuclei of neighbouring
molecules; holds large nonpolar molecules
together; very weak
• hydrogen bonds
– form when the slightly negative O or N that is
bonded to a slightly positive H is attracted to the
slightly positive H of a neighbouring molecule;
strongest
+
Water H
(H2O) –O A hydrogen
bond results
from the
H attraction
between the
+ partial positive
charge on the
– hydrogen atom
of water and
Ammonia the partial
(NH3) N negative charge
on the nitrogen
H H atom of
+ H + ammonia.
Figure 2.15
• dipole-dipole forces
– form when the slightly negative end of a polar
molecule is attracted to the slightly positive end of
a neighbouring polar molecule; stronger
– Occurs because electrons are in constant motion
and may accumulate by chance on one part of the
molecule. The result is “hot spots” of positive and
negative charge.
Water
• highly polar because of asymmetrical shape
and polar covalent bond
• The polarity of water molecules results in
hydrogen boding
–
+ Hydrogen
H bonds
+ – H
– +
+ –
Figure 3.2
“Like Dissolves Like”
• ionic compounds dissolve in water because
the ions separate
• However, molecules do not need to be ionic
to dissolve in water
• Smaller polar covalent molecules (eg: sugars,
alcohols) can dissolve in water, but large
nonpolar molecules (eg: oils) do not
• small nonpolar molecules (eg: O2, CO2) are
slightly soluble and need soluble protein
molecules to carry them (eg: hemoglobin
transports oxygen through the blood)
• hydrophilic – “water-loving;” dissolves in
water
– e.g. polar or ionic molecules, carbohydrates, salts
• hydrophobic – “water-fearing;” does not
dissolve in water
– e.g. non-polar molecules, lipids
Acids and Bases
• acid – donates H+ to water; pH 0-7
• base –donates OH- to water (or H3O); pH 7-14
• neutralization reaction – the reaction of an
acid and a base to produce water and a salt
(ionic compound)
Strong and Weak Acids/Bases
• strong acids and bases – ionize completely
when dissolved in water
– HCl(aq) (100% H3O+(aq))
– NaOH(aq) (100% OH-(aq))
• weak acids and bases – ionize only partially
when dissolved in water
– CH3COOH(aq) (1.3% H3O+(aq))
– NH3(aq) (10% OH-(aq))
Buffers
• The internal pH of most living cells must remain
close to pH 7
• Buffers
– Are substances that minimize changes in the
concentrations of hydrogen and hydroxide ions in a
solution
– Can donate H+ ions or remove H+ ions when
required
– E.g. carbonic acid creates bicarbonate ions (base) and
hydrogen ions (acid) (reversible reaction)
To Do
• Section 1.1 Questions
– Pg. 23 #1, 2, 4, 6-8, 12, 14, 15
