Biol 210 General Biology 1
Lecture 2
Review
Chemical Bonds
Atomic Structure
• Nucleus
– Protons, mass = 1, charge = +1
– Neutrons, mass = 1, charge = 0
• Electrons
–
–
–
–
Mass = negligible
Charge = -1
# e– = # protons
Outer shell (most energenic) e–’s form chemical bonds
Isotopes
Some isotopes are stable, such as 1H2
Other isotopes are unstable, such as 1H3.
When tritium decays, it gives off  particle.
Because the mass of an element includes the
average isotope abundance, the mass and
the atomic weight differ slightly
• Helium, He, atomic number 4, mass 4.003
•
•
•
•
Important Elements
• C HOPKINS CaFe Mg
–
–
–
–
–
–
–
–
–
–
–
C = carbon
H = hydrogen
O = oxygen
P = phosphorous
K = potassium
I = iodine
N = nitrogen
S = sulfur
Ca = calcium
Fe = iron
Mg = magnesium
Na = sodium
Cl = chloride
•Every atom has a characteristic total number
of covalent bonds that it can form = an
atom’s valence.
•The valence of hydrogen is 1.
•Oxygen is 2.
•Nitrogen is 3.
•Carbon is 4.
•Phosphorus should have a valence of 3, based
on its three unpaired electrons, but in biological
molecules it generally has a valence of 5,
forming three single covalent bonds and one
double bond.
Chemical Bonds
• Two atoms share one or more pairs of
valence electrons
• Four kinds of chemical bonds
–
–
–
–
Covalent
Hydrogen
Ionic
Van der Waals
• You must know the first 3 kinds
Covalent Bonds
• Two atoms share one or more pairs of
electrons
Covalent Bonds
• Two atoms share one or more pairs of
electrons
• Strongest chemical bond
Covalent Bonds
• Two atoms share one or more pairs of
electrons
• Strongest chemical bond
• 50-110 kcal/mol
Hydrogen molecule
•
•
•
•
Hydrogen atoms have one valence electron each
Innermost shell can accommodate two electrons
Each atom contributes an electron
Electrons effectively fill valence shell for both atoms
Oxygen
• Oxygen has 2 valence electrons
• Can share two pairs of electrons
• Two O atoms can form 2 covalent bonds
Oxygen + Hydrogen
• Oxygen can form bonds with hydrogen atoms
Oxygen + Hydrogen
• Oxygen can form bonds with hydrogen atoms
• Since H can only form one covalent bond
Oxygen + Hydrogen
• Oxygen can form bonds with hydrogen atoms
• Since H can only form one covalent bond
• O must bond two H atoms
Oxygen + Hydrogen
•
•
•
•
Oxygen can form bonds with hydrogen atoms
Since H can only form one covalent bond
O must bond two H atoms
H2O = water
Carbon
• Carbon has a valence of 4 electrons
Carbon
• Carbon has a valence of 4 electrons
• Can form 4 covalent bonds
Carbon
• Carbon has a valence of 4 electrons
• Can form 4 covalent bonds
• Biological molecules are largely carboncontaining molecules
Carbon
• Carbon has 4 valence electrons
• Can form 4 covalent bonds
• Biological molecules are largely carboncontaining molecules
• Organic = derived from organisms
Three p orbitals
Four hybrid orbitals
Z
s orbital
X
Y
Tetrahedron
(a) Hybridization of orbitals. The single s and three p orbitals of a valence
shell involved in covalent bonding combine to form four teardrop-shaped
hybrid orbitals. These orbitals extend to the four corners of an imaginary
tetrahedron (outlined in pink).
Figure 2.16 (a)
H—H
O=O
H—O—H
CH4
Carbon
Nitrogen
Hydrogen
Sulfur
Oxygen
Natural
endorphin
Morphine
(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to
receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.
Natural
endorphin
Brain cell
Morphine
Endorphin
receptors
(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell
recognize and can bind to both endorphin and morphine.
Ionic Bond
• Covalent bonds result from two atoms sharing
electrons
Ionic Bond
• Covalent bonds result from two atoms sharing
electrons
• Sometimes one atom “takes” the electron from
another atom.
Ionic Bond
• One atom has more protons than electrons = +1
Ionic Bond
• One atom has more protons than electrons = +1
• Other atom has one more electron than protons = 1
Ionic Bond
• One atom has more protons than electrons = +1
• Other atom has one more electron than protons = 1
• Opposite charges attract weakly (3-7 kcal/mol)
Hydrogen Bond
• We have studied two bonding extremes
Hydrogen Bond
• We have studied two bonding extremes
• Covalent bond = atoms share electrons
Hydrogen Bond
• We have studied two bonding extremes
• Covalent bond = atoms share electrons
• Ionic bond = one atom “take”s electrons
Hydrogen Bond
• Unequal e- sharing = partial charges on molecule
Hydrogen Bond
• Unequal e- sharing = partial charges on molecule
• Oxygen nucleus more attractive to electrons
Hydrogen Bond
• Unequal e- sharing = partial charges on molecule
• Oxygen nucleus more attractive to electrons
• Hydrogen nucleus less attractive
Hydrogen Bond
•
•
•
•
Unequal e- sharing = partial charges on molecule
Oxygen nucleus more attractive to electrons
Hydrogen nucleus less attractive
Partial charges, O more neg, H more pos
Hydrogen Bond
• Water = polar molecule
Hydrogen Bond
• Water = polar molecule
• Can interact weakly with other polar molecules
Hydrogen Bond
• Water = polar molecule
• Can interact weakly with other polar molecules
• H-bond 3-7 kcal/mol
Comparative Bond Strength
•
•
•
•
Covalent bond = 50-110 kcal/mol
Ionic bond = 3-7 kcal/mol
H-bond = 3-7 kcal/mol
van der Waals bond = ~1 kcal/mol
Compound
H 2O
H 2S
H2Te
MW
18
34
130
Boiling
Point
100°C
–60°C
–49°C
Predicted BP for water = -76°C
Compound
H 2O
H 2S
H2Te
MW
18
34
130
Boiling
Point
100°C
–60°C
–49°C
Predicted BP for water = -76°C
Predicted MP for water = -87°C
Compound
H 2O
H 2S
H2Te
MW
18
34
130
Boiling
Point
100°C
–60°C
–49°C
Predicted BP for water = -76°C
Predicted MP for water = -87°C
Temp. range for liquid water = 11°
Compound
H 2O
H 2S
H2Te
MW
18
34
130
Boiling
Point
100°C
–60°C
–49°C
Predicted BP for water = -76°C
Predicted MP for water = -87°C
Predicted temp. range for liquid water = 11°
Actual: 0–100°C
Compound
H 2O
H 2S
H2Te
MW
18
34
130
Boiling
Point
100°C
–60°C
–49°C
Predicted BP for water = -76°C
Predicted MP for water = -87°C
Predicted temp. range for liquid water = 11°
Actual: 0–100°C
Rationale: H-bonds
•The polarity of water molecules
–
Hydrogen
bonds
+
H
+
Figure 3.2
–
–
+
H
+
–
•The polarity of water molecules
–Allows them to form hydrogen bonds with each other
–
Hydrogen
bonds
+
H
+
Figure 3.2
–
–
+
H
+
–
•The polarity of water molecules
–Allows them to form hydrogen bonds with each other
–Contributes to the various properties water exhibits
–
Hydrogen
bonds
+
H
+
Figure 3.2
–
–
+
H
+
–
• The different regions of the polar water
molecule can interact with ionic compounds
called solutes and dissolve them
–
Na+
+
–
–
Na+
Cl–
+
Cl –
–
+
+
–
Figure 3.6
–
+
+
–
–
+
+
–
–
• 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+
+
–
–
Na+
Cl–
+
Cl –
–
+
+
–
Figure 3.6
–
+
+
–
–
+
+
–
–
• 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+).
Positive
hydrogen regions
of water molecules
cling to chloride anions
(Cl–).
–
Na+
+
–
–
Na+
Cl–
+
Cl –
–
+
+
–
Figure 3.6
–
+
+
–
–
+
+
–
–
• Water can also interact with polar
molecules such as proteins
–
+
This oxygen is
attracted to a slight
positive charge on
the lysozyme
molecule.
This oxygen is attracted to a slight
negative charge on the lysozyme molecule.
Figure 3.7
(a) Lysozyme molecule
in a nonaqueous
environment
(b) Lysozyme molecule (purple)
in an aqueous environment
such as tears or saliva
(c) Ionic and polar regions on the protein’s
Surface attract water molecules.
pH
• Water can dissociate
–
+
H
H
H
H
Figure on p. 53 of water
dissociating
H
H
H
Hydronium
ion (H3O+)
+
H
Hydroxide
ion (OH–)
pH
• Water can dissociate
– Into hydronium ions and hydroxide ions
–
+
H
H
H
H
Figure on p. 53 of water
dissociating
H
H
H
Hydronium
ion (H3O+)
+
H
Hydroxide
ion (OH–)
pH
• Water can dissociate
– Into hydronium ions and hydroxide ions
• Changes in the concentration of these ions
–
+
H
H
H
H
Figure on p. 53 of water
dissociating
H
H
H
Hydronium
ion (H3O+)
+
H
Hydroxide
ion (OH–)
pH
• Water can dissociate
– 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
Figure on p. 53 of water
dissociating
H
H
H
Hydronium
ion (H3O+)
+
H
Hydroxide
ion (OH–)
• The pH scale and pH values of various
aqueous solutions
Increasingly Acidic
[H+] > [OH–]
pH Scale
0
Increasingly Basic
[H+] < [OH–]
Neutral
[H+] = [OH–]
Figure 3.8
1 Battery acid
2 Digestive (stomach)
juice, lemon juice
3 Vinegar, beer, wine,
cola
4 Tomato juice
5 Black coffee
Rainwater
6 Urine
7 Pure water
8
9
10
11
12
13
14
Human blood
Seawater
Milk of magnesia
Household ammonia
Household bleach
Oven cleaner
• The pH scale and pH values of various
aqueous solutions
Increasingly Acidic
[H+] > [OH–]
pH Scale
0
Increasingly Basic
[H+] < [OH–]
Neutral
[H+] = [OH–]
Figure 3.8
1 Battery acid
2 Digestive (stomach)
juice, lemon juice
3 Vinegar, beer, wine,
cola
4 Tomato juice
5 Black coffee
Rainwater
6 Urine
7 Pure water
8
9
10
11
12
13
14
Human blood
—pH 7.4
Seawater
Milk of magnesia
Household ammonia
Household bleach
Oven cleaner