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Chapter 02
Molecules of Life
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1
Why Study Chemistry?
 The science that deals with the basic properties of
matter
 Chemical substances undergo changes and interact
with one another in chemical reactions
 Metabolism is the use of nutrients for energy or for
making substances of cells
 Understanding the basic principles of chemistry is
essential to understanding metabolic processes in
living things Understanding microbial metabolism aids
understanding human metabolism
A Glimpse of History
 Louis Pasteur (1822–1895) often considered
father of bacteriology
 Started career as chemist for French wine
industry
 Studied tartaric and paratartaric acids
•
•
•
•
Form thick crusts within wine barrels
Identical chemical composition
Affect polarized light differently
Observed paratartaric acid crystals had two different
structures
• Realized paratartaric acid composed of mixture of
stereoisomers
Atoms and Elements
 Atoms
• Basic unit of all matter
• Made up of three
major components
• Protons
– Positively charged
• Electrons
– Negatively charged
• Neutrons
– Uncharged
Atoms and Elements
 Atom
• Protons and neutrons are found in the nucleus
• Account for the “weight” of the atom
– Atomic mass
• Electrons orbit the nucleus
= # of Protons + # of Neutrons
• Have relatively little mass
– Do not contribute to the mass of the atom
» Approximately 2,000 electrons = 1 proton
• Protons and electrons are equal in a uncharged atom
i.e.,complete atom
2.1. Atoms and Elements
 Atoms distinguished by atomic number
• Number of protons in nucleus
 Also atomic mass
Protons ONLY
PROTONS + NEUTRONS
• Sum of protons and neutrons (electrons too light)
• E.g., hydrogen (one proton, no neutrons) has atomic
number and mass of 1
2.1. Atoms and Elements
 Elements consist of only one type of atom
• Cannot be chemically separated into simpler parts
• Living matter primarily composed of four
• Hydrogen, carbon, oxygen, nitrogen
• Atoms of an element can have different mass numbers
• Same # of protons, different # of neutrons
• Termed isotopes
2.1. Atoms and Elements
 Electrons are arranged in shells around nucleus
• First shell can hold up to 2
• Next and subsequent shells
can hold up to 8
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• Inner shells (closer to nucleus)
fill first
6e–
6p+
6n0
(a)
• Biological molecules follow
“octet rule”
Mass
number
• Most stable with full outer shell
• Electrons farther from nucleus
have higher energy level
• Valence electrons are those in
outer shell
Atomic
number
12
6
C
(b)
C
• Important in bond formation
(c)
Element
symbol
Structure of Four Biologically Important
Atoms
Chemical Bonds and the Formation of Molecules
 Atoms are most stable when the outer orbital
contains the maximum number of electrons
• 2, 8, 8 etc.
 To fill outer orbitals atoms form bonds with other
atoms to fill outer orbitals
• Bonds are formed with the sharing or the gain or loss
of electrons
• Molecules are formed when atoms bond together
Chemical Bonds and the Formation of Molecules
 There are several types of chemical bonds
• They also vary in strength
 Chemical bonds include
• Covalent bonds
• Ionic bonds
• Hydrogen bonds
Covalent Bonds
 Covalent bonds form when atoms share electrons
• One pair of shared electrons = one covalent bond
• Carbon bonds with hydrogen to form organic molecules
• Other compounds are
inorganic
• Covalent bonds
are strong
• Difficult to break at
biological
temperatures
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H
4
H
+
Each hydrogen atom
needs one electron
to fill its valence.
C
Carbon needs
four electrons
to fill its valence.
H
C H
H
Methane
(a)
H
• Requires enzymes
H
C
CH4
H
H
Each line represents
a shared pair
of electrons.
(b)
Ball-and-stick
model
Space-filling
model
Chemical
formula
Covalent Bonds
 Achieve stability through the
sharing of electrons between
atoms
• Creates a strong bond
• Difficult to break
• Requires significant energy
usually in the form of heat
• Never break spontaneously at
physiological temperatures
– Enzyme required to break at
lower temperature
• Bonds can be polar or non-polar
Covalent Bonds
 Non-polar and Polar
• Covalent bonds may have
an equal or unequal
attraction for the shared
electrons
• Non-polar covalent
• Bonds formed between
identical atoms or
between atoms that
have similar attraction
– H-H or C-H
Covalent Bonds
• Polar covalent bond
• One atom has a greater
attraction to the electrons
than the other
– Produces a slight charge
within the molecule
» One part of the
molecule with be
slightly negatively
charged and one
molecule with by
slightly positively
charged
• Electrons are unequally
shared
Covalent Bonds
 Covalent bonds can be non-polar or polar
• Non-polar: equal sharing of electrons
• Polar: unequal sharing of electrons
• One atom more electronegative
than other
• Important in biological systems
– Result in hydrogen bonds
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–
O H
H
(a)
+
(b)
+
Increasing
electron density
Decreasing
electron density
Ionic Bonds
 Formed by atoms gaining or losing
electrons to obtain stability
• Electrons completely leave first
atoms and become part of
outer orbital of second atom
• Loss and gain of electrons
leads to charged atoms
(ions)
– Atom that loses electrons
becomes positively charged
– Atom that gains electron
becomes negatively charged
 Charged atoms are attracted to
each other and form a bond
between ions (opposites attract)
• Ionic bond
Ionic Bonds
 Ionic bonds formed by atoms gaining or losing
electrons
• Produces charged atoms, or ions
• Cations (positive charge)
• Anions (negative charge)
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
e–
Na
 Ionic bonds form because
Na+
of strong attraction
between negative and
+
Na
positive charges
• Relatively weak bonds
Cl
Cl
Cl
–
–
(a)
(b)
Na
Cl
Na+
Cl–
Ionic Bonds
 Ionic bonds are weaker than covalent bonds
• Bonds dissociate in water
• Easily broken at room temperature
• Approximately 100 time weaker than covalent bonds
 Important among weak forces holding biological
molecules together
Hydrogen Bonds
 Weak bonds formed from the attraction of positively charged
hydrogen atoms
• Hydrogen atoms in polar molecules are attracted to
negatively charged atoms or molecules
• Most commonly oxygen or nitrogen
• Hydrogen bonds occur between molecules such as water
and DNA
• Covalent bonds are formed within the molecules
– Hydrogen bonds hold molecules together
– Covalent bonds hold atoms together
Molarity
 A mole is 6.022 x 1023 particles
• A mole of one compound has the same # of molecules
as a mole of any other
• E.g., 1 mole NaCl = 58.4 g; 1 mole KCl = 74.55 g
• Each example has a different mass, but the same
number of molecules!
 Molarity (M) of solution is # moles dissolved in
1 liter H2O
• E.g., a 1 M solution of NaCl is 58.4 g dissolved in
1 liter H2O
To calculate one mole of NaCl:
∑ Na = 22.9 + Cl= 35.5
=
58.4 g
Hydrogen bonds

Hydrogen bonds
• Form between hydrogen and
other electronegative elements
(O or N)
• Increased number provides
stability to molecules
Water: a polar molecule
Hydrogen
Bonding
Polar Compounds and Hydrogen Bonding
Chemical Compounds of the Cell
 Most important molecule is water
• Importance of water depends on its unusual bonding
properties
2.3. Chemical Components of the Cell
 Water
• Makes up over 70% of all
living organisms by weight
• Polar molecule
• Hydrogen bonding explains
properties
• Ice: each water molecule
forms 4 hydrogen bonds
• Liquid: hydrogen bonds
continually form and break
Water molecule
–
+
+
Ice
Liquid water
Water as a Biological Solvent

Polarity
• Cytoplasm is aqueous and contains polar
molecules
• Promotes hydrogen bonding (stability)
• Promotes interaction within biomolecules
• Forces nonpolar molecules (lipids) to aggregate

Cohesiveness
• H bonds are dynamic: forming, breaking, re-forming
• Responsible for water’s important properties:
1. High surface tension,
2. High specific heat
3. Surface ice insulates underlying water – prevents
freezing (aquatic organisms can survive)
Water
 Polar nature makes water
an excellent solvent
• Dissolves polar compounds
and those with +/– charge
• These compounds are
hydrophillic
• “Water loving”
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– –
Na+ –
–


–

Water molecules
• Non-polar molecules are
hydrophobic
Na+
• “Water fearing”
Cl–
• Water with dissolved
substances freezes at
lower temperatures
+
+
+
Salt crystal (NaCl)
Cl–
+
+
Polarity and Water Molecules
Positive polar end of
water surrounds the
negative ions
Negative polar end of
water surrounds the
positive ions
Hydrogen Bonding Between Water Molecules
2D surface hydrogen bonds
are stronger than the 3D in
the middle of the volume
Strong Surface Tension of Water
Acids, Bases, and pH
 Acid: A hydrogen ion (H+) or proton donor
 Base: A proton acceptor, or a hydroxyl
ion (OH-) donor
 pH scale: relates proton concentration to
pH (logarithmic scale)
pH= log (1/[H+ ]
The molar concentration of H+
pH of Aqueous Solutions
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
• Ten-fold increase in [H+]
decreases [OH–] by factor of
ten
10–14
14
1MNaOH
Drain cleaner
13
More basic (higher pH)
• Water tends to split into
(acidic) and OH– (basic)
• Pure water has equal
concentrations (each 10–7 M)
• Product of [H+] and [OH–] is
always 10–14 M
H+
pH
H+ ion concentration
(molarity)
10–7
More acidic (lower pH)
 pH is measure of [H+] in m/l
• Each log unit represents tenfold change in [H+]
• Buffers stabilize pH of
solutions
12
Lye
Household ammonia
11
Milk of magnesia
10
Detergent solution
9
8
Seawater
7
Blood
NEUTRAL
6
Milk
Urine
Unpolluted rainwater
5
Black coffee
Beer
4
Vinegar
3
Cola
Lemon juice
2
Stomach acid
1
100
0
Battery acid
pH Values of Some Common
Substances
Elements and Small Molecules in Cell
 ~1% dry weight is
inorganic ions
•
•
•
•
•
•
•
•
Na+ (sodium)
K+ (potassium)
Mg2+ (magnesium)
Ca2+ (calcium)
Fe2+ (iron)
Cl– (chloride)
PO43– (phosphate)
SO42– (sulfate)
 Organic compounds
• Have important
functional groups
Elements and Small Molecules in Cell
 Adenosine triphosphate (ATP)
• Energy currency of cell
• Three negatively charged phosphate groups repel
•
•
•
•
Bonds inherently unstable, easily broken
Releases energy to drive cellular processes
High energy phosphate bonds denoted by ~
ATP  ADP + Pi
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Adenosine
NH2
N
Phosphate groups
N
O
O–
P
O–
O
O
P
O–
High-energy
bonds
O
O
P
O–
O
CH2
N
O
OH OH
Ribose
N
Adenine
Macromolecules and Their Component
Parts
 Macromolecules are very large
• Macro = large
 Biological macromolecules are divided into four
classes
•
•
•
•
Proteins
Polysaccharides (carbohydrates)
Lipids
Nucleic acids
Macromolecules and Their
Component Parts
 All macromolecules are
polymers
• Poly = many
• Large molecules
formed by joining
smaller subunits
together
• Joining subunits
together involves
dehydration reaction
– H2O is removed
during chemical
reaction
» Reaction
termed
dehydration
synthesis
Macromolecules and Their
Component Parts
 Macromolecules are
broken down into
smaller subunits
• Instead of removing
H2O, a molecule of
H2O is added
• Reaction termed
hydrolytic reaction or
hydrolysis
Dehydration Synthesis
A new molecule is synthesized
H
OH
H
OH
Dehydration Synthesis
OH
H H2O OH
H
2 Separate molecules to be joined
Water comes out = Dehydration
2.4. Proteins
 Proteins
 More than half of dry weight of cell
 Versatile, many important roles
•
•
•
•
•
•
Catalyze reactions
Transport molecules
Move cells
Provide cellular framework
Sense and respond to conditions outside cell
Regulate gene expression
Amino Acids
 Proteins made up of amino acids
•
•
•
•
Infinite possible combinations of 20 amino acids
Protein characteristics depend mainly on shape
Shape determined by amino acid sequence
Amino acids share common structure
• Side chain (R group) differs
• All except glycine exist as stereoisomers
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D-Amino acid
L-Amino acid
X
W
W
C
C
Y
Y
X
Side chain—
“R” is the general
designation for a side chain
R
H
Amino group—
positively charged
at neutral pH
Mirror
H
O
N+
C
H
H
C
O–
Carboxyl group—
negatively charged
at neutral pH
Amino Acid Subunits
 All amino acids have
the following shared
features
• A carboxyl group
(COO-)
• An amino group (NH2+)
• A central carbon
• A side chain
• The side chain
differentiates the
amino acids
• Amino acids are subdivided
based on similarities of the
side chain
Peptide Bonds and Their Synthesis
 The amino acids that form
proteins are held together by
peptide bonds
• Unique type of covalent
bond
• Formed between the
interaction of the
carboxyl group of one
amino acid and the
amino group of the
following amino acid
– Reaction causes the
release of water and
the formation of a
peptide bond
Hydrolysis (lysis, i.e. break apart with water)
End with separate amino acids
Starting with peptide bonded amino acids
O
|
|
||
N- C - C -
H
H
|
|
H
R1
H
H
|
|
N - C
|
|
|
R2
O
||
-C
|
OH
Water has been used to
break (lyse) a bond
This is called Hydrolysis
break peptide bond and add water parts
HOH
H2O
Break water bonds
Bring in water
Protein Structure
Primary Structure
R
Determinants:
 Hydrogen
bonding
Secondary Structure
 Polar
groups
 Non-polar
groups
 Covalent
Tertiary Structure
bonds
C
C
H
O
H
H
O
N
C
C
R
R
N
C
C
H
H
O
H
H
N
C
R
The primary structure can fold
into a pleated sheet, or turn into a helix.
(a)
Secondary Structure
-pleated sheet
-helix
(b)
(c)
Quaternary Structure
(d)
Protein Structure
 Proteins have four
structures
•
•
•
•
Primary
Secondary
Tertiary
Quaternary
Protein Structure
 Primary structure
• Sequence of amino acids
• In large part determines other protein features
Protein Structure
 Secondary structure
• Primary structure folds
into new configuration
• Helical structure
– Alpha (α) helix
• Pleated structure
– Beta (β) sheet
• New configuration
results from weak
bonds formed between
amino acids
Protein Structure
 Tertiary structure
• 3 dimensional
structure
• 2 major shapes
• Globular
• Fibrous
• Becomes functional
protein
Protein Denaturation
 Proteins must have specific
shape to have proper
function
• Environmental conditions
can break bonds within
the protein
• Causes shape change
– Shape change causes
protein to stop
functioning
» Called
denaturation
 Denaturation can be
reversible or irreversible
• Environment determines
reversibility
Carbohydrates
 Carbohydrates are diverse group of molecules
with various sizes
 Play important roles in all organisms including
• Common source of food and energy
• Form part of nucleic acids
• Form part of bacterial cell wall
Carbohydrates
 Carbohydrates contain carbon, hydrogen and oxygen in
1:2:1 ratio
• Each carbon atom is bound to two hydrogen atoms and
one oxygen atom
• CH2O
 Polysaccharide
• large molecules made of carbohydrate molecules
 Oligosaccharide
• short chains of carbohydrates
 Monosaccharide
• Single carbohydrate molecule
Carbohydrates
 Monosaccharide
• Classified by number of carbons in molecule
• Most common monosaccharides
• 5 and 6 carbon sugars
– 5 carbon sugars = pentose
» Ribose and deoxyribose
– 6 carbon sugars = hexose
» Glucose, fructose and galactose
Carbohydrates
 Disaccharides
• Produced by joining two monosaccharides through
dehydration synthesis
• Lactose and sucrose most common in nature
• Glucose + galactose = lactose
• Glucose + fructose = sucrose
• Maltose less common
• Glucose + glucose = maltose
2.5. Carbohydrates
 Monosaccharides have single unit
• 5-carbon include ribose, deoxyribose
• 6-carbon include glucose, galactose, fructose, mannose
• Structural isomers: distinct properties, names
• Can exist in alpha (α) or beta (β) form depending on
location of hydroxyl group
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6
CH2OH
O
5
H
OH
H
1
OH
HO
4
H
H
3
OH
H
H
1
2 OH
OH
α form
5 CH2OH
O
4
H
H
3
OH
H
1
2 H
OH
OH
β form
6
OH
H
Galactose
2
OH
CH2OH
O
H
1
H
H
3
H
Mannose
O
OH
2
H
OH
HO H
4
OH
3
CH2OH
6
5
OH
H
1
OH
Glucose
5 CH2OH
O
O
H
2
3
Ribose
H
4
H
HO
CH2OH
5
H
H
4
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6
5
H
OH
OH
H
3
4
OH
H
Fructose
2
1
CH2OH
Carbohydrates
 Polysaccharides
• Serve different function
• Cellulose most abundant organic molecule on earth
• Polymer of glucose molecules
• Principle constituent in plant cell wall
• Glycogen is carbohydrate storage molecule of animals and
some bacteria
• Polymer of glucose subunits
• Dextran storage molecule for carbon and energy for some
bacteria
• Polymer of glucose subunits
Cellulose
Starch
Nucleic Acids
 Two types of nucleic acid
• DNA
• Carry genetic code in all cells
• RNA
• Decodes sequence of amino acids to produce proteins
• Sub units of nucleic acids are nucleotides
DNA
 Master molecule
• Determines specific properties
of the cell
 Nucleotides are composed of
three units
• Nitrogen containing ring
compound
• Nitrogenous base
– Purine
» Adenine and guanine
– Pyrimidine
» Thymine and cytosine
• Five carbon sugar molecule
• Deoxyribose
• Phosphate molecule
DNA
 Nucleotides are joined through
covalent bonding
• Bond created between
phosphate of one
nucleotide and sugar of the
adjacent through
dehydration synthesis
• Phosphate molecule acts
as a bridge between the
number 3 (3’) carbon of
one sugar and the
number 5 (5’) carbon of
the adjacent
– Results in a sugar
phosphate backbone
2.6. Nucleic Acids
 Nucleotides include nucleobase
• Purines adenine (A), guanine (G)
• Two fused rings
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• Pyrimidines cytosine (C),
thymine (T)
• Single ring structure
• Uracil (U) is found only
in RNA
Purines
(double ring)
Pyrimidines
(single ring)
O
NH2
N
H
CH3
N
N
H
H
N
H
N
H
Adenine (A)
(both DNA and RNA)
H
H
Thymine (T)
(DNA only)
NH2
O
N
O
N
H
H
NH2
H
N
N
H
N
N
H
Guanine (G)
(both DNA and RNA)
N
O
H
Cytosine (C)
(both DNA and RNA)
H
H
Uracil (U)
(RNA only)
H
DNA
 DNA in living organisms is a double stranded
helical molecule
• Strands are held together by hydrogen bonding
between the nitrogen bases
• Specific pairing between bases
– Adenine binds to thymine
» A-T or T-A
– Guanine binds to cytosine
» G-C or C-G
• Bases are complementary
RNA
 Involved in decoding DNA
 Structure is similar to DNA
• Differs in a number of ways
• Thymine is replaced by uracil
– There is no thymine base in RNA
• The sugar is ribose in place deoxyribose
• RNA is generally shorter
• Exists as a single stranded molecule not double
stranded
2.7. Lipids
 Lipids are non-polar, hydrophobic molecules
• Diverse group defined by this physical property
• Highly soluble in organic solvents
• E.g., ether, benzene, chloroform
• Not composed of similar subunits
 Simple lipids contain carbon, hydrogen, oxygen
• Fats most common
• Glycerol linked to fatty
acids via dehydration
synthesis
• Fatty acids are long chains
of bonded C, H atoms with
carboxyl group at one end
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
H
O
H C OH
HO
C
R
3 H2O
H
O
H C O
C
O
H C OH
+
HO
C
O
R
HO
C
R
H
Glycerol
(b)
H C O
Dehydration
synthesis
O
H C OH
R
C
R
O
H C O
C
R
H
+
3 fatty acids
Triglyceride (fat)
Lipids
 Critical component of the cell membrane
• Membranes act a gatekeepers to the cell
• Often determines what enters or leaves the cell
 Heterogeneous group of molecules
• Made up of different subunits
 Defining feature
• Insoluble in water
 Smallest of the four macromolecules
 Can be divided into two general classes
• Simple lipids
• Compound lipids
Simple Lipids
 Contain only carbon, hydrogen
and oxygen
 Most common are called fats
• Solid at room temperature
• Made of glycerol and fatty
acids
• Fatty acids are long
hydrocarbon chains plus
an acid group (COOH) at
the end
• Glycerol is carbon
hydrogen chain with
three hydroxyl (OH)
groups attached
– Allows for the binding of
three fatty acids to one
glycerol
» Triglyceride
• Fatty acids bond to glycerol
covalently through dehydration
synthesis
2.7. Lipids
 Fatty acids: two groups
• Saturated: no double bonds
• Tails pack tightly so solid at
room temperature (fats)
• Unsaturated: double bonds
• Kinks prevent tight packing
so liquid at room
temperature (oils)
• Monounsaturated: 1 double
bond
• Polyunsaturated: >1 double
bond
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Saturated fatty acid (palmitic acid)
HO
O
H H H H H H H H H H H H H H H
C
C C C C C C C C C C C C C C C H
H H H H H H H H H H H H H H H
Unsaturated fatty acid (oleic acid)
Double bond
(a)
• Most natural fatty acids are cis: hydrogens attached to same side of double
bond
• Trans have hydrogens on opposite sides of double bond
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
2.7. Lipids
Watery exterior of cell
Phospholipid
bilayer
 Compound lipids include
other elements
 Phospholipids important
• Phosphate group linked to
polar molecule
• Yields hydrophilic head group
• Hydrophobic fatty acid tails
• Form lipid bilayer with polar
heads oriented outward toward
aqueous environments
• Essential component of cytoplasmic
membranes
 Lipoproteins, lipopolysaccharides
also compound lipids
Watery interior of cell
Phospholipid
R
Polar head
group
O
P O–
O
Hydrophilic
head
Hydrophobic
tail
Phosphate
group
O
CH2
CH CH2
O
O
C
O C
CH2
Glycerol
O
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH
CH2
CH2
CH2
CH
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
Saturated fatty acid
CH2
CH2
CH2
CH2
CH2
CH3
Unsaturated fatty acid
Simple Lipids
 Steroids are also considered
simple lipids
 Differ from fats in structure
and function
• Structure consists of fourmembered ring
 Classified as lipid because
steroids are insoluble in
water
 If one of the rings has a
hydroxyl (OH) group
attached it is classified as a
sterol
• Example: cholesterol