Chapter 2:
Chemistry of Life
(Chemistry Comes Alive)
Niels Bohr – originator of the
model of the atom we
utilize in BIOL 232 & BIOL 233..
Selman Waksman
He investigated how soil microbes defended themselves against invaders which
lead to the He and coworkers isolation of twenty-two different defensive
compounds produced by soil microbes. These discoveries lead to the discovery
streptomycin, the first antibiotic effective against tuberculosis. Waksman received
the 1952 Nobel Prize in physiology or medicine.
Chemistry still plays a significant role in
the cutting-edge research into
physiology today. Researchers with
deep understanding of chemistry are
needed in medicine, physiology, and
related fields.
Figure 2.1 Two models of the structure of an atom.
Nucleus
Nucleus
Helium atom
Helium atom
2 protons (p+)
2 neutrons (n0)
2 electrons (e–)
2 protons (p+)
2 neutrons (n0)
2 electrons (e–)
(a) Planetary model
Proton
Neutron
(b) Orbital model
Electron
Electron
cloud
Figure 2.2 Atomic structure of the three smallest atoms.
Proton
Neutron
Electron
Hydrogen (H)
(1p+; 0n0; 1e–)
Helium (He)
(2p+; 2n0; 2e–)
Lithium (Li)
(3p+; 4n0; 3e–)
Figure 2.3 Isotopes of hydrogen.
Proton
Neutron
Electron
Hydrogen (1H)
(1p+; 0n0; 1e–)
Deuterium (2H)
(1p+; 1n0; 1e–)
Tritium (3H)
(1p+; 2n0; 1e–)
Figure 2.5 Chemically inert and reactive elements.
(a)
Chemically inert elements
Outermost energy level (valence shell) complete
8e
2e
Helium (He)
(2p+; 2n0; 2e–)
(b)
2e
Neon (Ne)
(10p+; 10n0; 10e–)
Chemically reactive elements
Outermost energy level (valence shell) incomplete
4e
1e
Hydrogen (H)
(1p+; 0n0; 1e–)
2e
Carbon (C)
(6p+; 6n0; 6e–)
1e
6e
2e
Oxygen (O)
(8p+; 8n0; 8e–)
8e
2e
Sodium (Na)
(11p+; 12n0; 11e–)
Figure 2.6 Formation of an ionic bond.
Sodium atom (Na)
(11p+; 12n0; 11e–)
Chlorine atom (Cl)
(17p+; 18n0; 17e–)
+
–
Sodium ion (Na+)
Chloride ion (Cl–)
Sodium chloride (NaCl)
(a) Sodium gains stability by losing one electron, and
chlorine becomes stable by gaining one electron.
CI–
Na+
(c) Large numbers of Na+ and Cl– ions
associate to form salt (NaCl) crystals.
(b) After electron transfer, the oppositely
charged ions formed attract each other.
Figure 2.7 Formation of covalent bonds.
Reacting atoms
Resulting molecules
+
or
Structural formula
shows single bonds.
Hydrogen atoms
Carbon atom
Molecule of methane gas (CH4)
(a) Formation of four single covalent bonds:
Carbon shares four electron pairs with four
hydrogen atoms.
+
or
Structural formula
shows double bond.
Oxygen atom
Oxygen atom
Molecule of oxygen gas (O2)
(b) Formation of a double covalent bond: Two
oxygen atoms share two electron pairs.
+
or
Structural formula
shows triple bond.
Nitrogen atom
Nitrogen atom
(c) Formation of a triple covalent bond: Two
nitrogen atoms share three electron pairs.
Molecule of nitrogen gas (N2)
Figure 2.8 Carbon dioxide and water molecules have different shapes, as illustrated by molecular models.
Figure 2.9 Ionic, polar covalent, and nonpolar covalent bonds compared along a continuum.
Figure 2.10 Hydrogen bonding between polar water molecules.
+
–
Hydrogen bond
(indicated by
dotted line)
+
+
–
–
–
+
+
+
–
(a) The slightly positive ends (+) of the water molecules become
aligned with the slightly negative ends (–) of other water
molecules.
(b) A water strider can walk on a pond because of the high
surface tension of water, a result of the combined
strength of its hydrogen bonds.
Figure 2.13 The pH scale and pH values of representative substances.
Concentration
(moles/liter)
Examples
[OH–]
[H+]
pH
100
10–14
14
1M Sodium
hydroxide (pH=14)
10–1
10–13
13
Oven cleaner, lye
(pH=13.5)
10–2
10–12
12
10–3
10–11
11
10–4
10–10
10
10–5
10–9
9
10–6
10–8
8
10–7
10–7
7 Neutral
10–8
10–6
6
10–9
10–5
5
10–10
10–4
4
10–11
10–3
3
10–12
10–2
2
10–13
10–1
1
10–14
100
0
Household ammonia
(pH=10.5–11.5)
Household bleach
(pH=9.5)
Egg white (pH=8)
Blood (pH=7.4)
Milk (pH=6.3–6.6)
Black coffee (pH=5)
Wine (pH=2.5–3.5)
Lemon juice; gastric
juice (pH=2)
1M Hydrochloric
acid (pH=0)
Figure 2.12 Dissociation of salt in water.
+
–
+
Water molecule
Salt crystal
Ions in solution
Figure 2.16c Lipids.
(c)
Simplified structure of a steroid
Four interlocking hydrocarbon rings form a steroid.
Example
Cholesterol (cholesterol is the
basis for all steroids formed in the body)
Figure 2.19 Levels of protein structure.
Amino acid
Amino acid
Amino acid
Amino acid
Amino acid
(a) Primary structure:
The sequence of
amino acids forms the
polypeptide chain.
(b) Secondary structure:
The primary chain forms
spirals (-helices) and
sheets (-sheets).
-Helix: The primary chain is coiled
to form a spiral structure, which is
stabilized by hydrogen bonds.
-Sheet: The primary chain “zig-zags” back
and forth forming a “pleated” sheet. Adjacent
strands are held together by hydrogen bonds.
(c) Tertiary structure:
Superimposed on secondary structure.
-Helices and/or -sheets are folded up
to form a compact globular molecule
held together by intramolecular bonds.
(d) Quaternary structure:
Two or more polypeptide chains, each
with its own tertiary structure, combine
to form a functional protein.
Tertiary structure of prealbumin
(transthyretin), a protein that
transports the thyroid hormone
thyroxine in serum and cerebrospinal fluid.
Quaternary structure of a
functional prealbumin molecule.
Two identical prealbumin subunits
join head to tail to form the dimer.
Figure 2.19a Levels of protein structure.
Amino acid
Amino acid
Amino acid
Amino acid
Amino acid
(a) Primary structure:
The sequence of amino acids forms the polypeptide chain.
Figure 2.19b Levels of protein structure.
-Helix: The primary chain is coiled
to form a spiral structure, which is
stabilized by hydrogen bonds.
-Sheet: The primary chain “zig-zags” back
and forth forming a “pleated” sheet. Adjacent
strands are held together by hydrogen bonds.
(b) Secondary structure:
The primary chain forms spirals (-helices) and sheets (-sheets).
Figure 2.19c Levels of protein structure.
Tertiary structure of prealbumin
(transthyretin), a protein that
transports the thyroid hormone
thyroxine in serum and cerebrospinal fluid.
(c) Tertiary structure:
Superimposed on secondary structure. -Helices and/or -sheets are
folded up to form a compact globular molecule held together by
intramolecular bonds.
Figure 2.19d Levels of protein structure.
Quaternary structure of
a functional prealbumin
molecule. Two identical
prealbumin subunits
join head to tail to form
the dimer.
(d) Quaternary structure:
Two or more polypeptide chains, each with its own tertiary structure,
combine to form a functional protein.
An example of the progression in complexity of structure in proteins with the final
quaternary structure being that of hemoglobin.
Figure 2.20 Enzymes lower the activation energy required for a reaction to proceed rapidly.
WITHOUT ENZYME
WITH ENZYME
Activation
energy
required
Less activation
energy required
Reactants
Reactants
Product
Product
Figure 2.21 Mechanism of enzyme action.
Substrates (S)
e.g., amino acids
+
Product (P)
e.g., dipeptide
Energy is
absorbed;
bond is
formed.
Water is
released.
Peptide
bond
Active site
Enzyme (E)
Enzyme-substrate
complex (E-S)
1 Substrates bind
2 Internal
at active site.
rearrangements
Enzyme changes
leading to
shape to hold
catalysis
substrates in
occur.
proper position.
Enzyme (E)
3 Product is
released. Enzyme
returns to original
shape and is
available to catalyze
another reaction.
Substrate “fits”
with active site
Substrate unable to bind
Active site
Denatured enzyme
Functional
enzyme
(a)
(b)
Active site
Amino acids
+
Enzyme (E)
Substrates (S)
Enzyme-substrate
complex (E-S)
H2O
Free enzyme (E)
Peptide bond
Internal rearrangements
leading to catalysis
Dipeptide product (P)
Figure 2.22 Structure of DNA.
Phosphate
Sugar:
Deoxyribose
Base:
Adenine (A)
Thymine (T)
Adenine nucleotide
Sugar
Phosphate
Thymine nucleotide
Hydrogen
bond
(a)
Sugar-phosphate
backbone
Deoxyribose
sugar
Phosphate
Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)
(b)
(c) Computer-generated image of a DNA molecule
Figure 2.23 Structure of ATP (adenosine triphosphate).
High-energy phosphate
bonds can be hydrolyzed
to release energy.
Adenine
Phosphate groups
Ribose
Adenosine
Adenosine monophosphate (AMP)
Adenosine diphosphate (ADP)
Adenosine triphosphate (ATP)
Figure 2.24 Three examples of cellular work driven by energy from ATP.
Solute
+
Membrane
protein
(a) Transport work: ATP phosphorylates transport
proteins, activating them to transport solutes
(ions, for example) across cell membranes.
+
Relaxed smooth
muscle cell
Contracted smooth
muscle cell
(b) Mechanical work: ATP phosphorylates
contractile proteins in muscle cells so the
cells can shorten.
+
(c) Chemical work: ATP phosphorylates key
reactants, providing energy to drive
energy-absorbing chemical reactions.
Table 2.1 Common Elements Composing the Human Body (1 of 2)
Notice how there are three broad categories of
these elements, major, lessor, and trace.
Table 2.1 Common Elements Composing the Human Body (2 of 2)