Transcript Foundations in Microbiology Seventh Edition

Chapter 2
The Chemistry of
Biology
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1
Atoms, Bonds, and Molecules
• Matter - all materials that
occupy space and have
mass. Matter is composed
of atoms
• Atom - simplest form of
matter not divisible into
simpler substances
– Protons:
(+) subatomic particles
– Neutrons:
neutral subatomic
particles
– Electrons:
(-) subatomic particles
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Nucleus
1 proton
1 electron
Hydrogen
Shells
Nucleus
proton
Nucleus
6 protons
6 neutrons Carbon
6 electrons
neutron
electron
(b)
2
Different Types of Atoms
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• All atoms share the
same fundamental
structure
• Element - pure
substances with a
characteristic number
of protons, neutrons,
and electrons and
predictable chemical
behaviors
Nucleus
1 proton
1 electron
Hydrogen
Shells
Nucleus
proton
Nucleus
(b)
6 protons
6 neutrons Carbon
6 electrons
neutron
electron
3
The Major Elements of Life
4
Characteristics of Elements
Atomic number – number of
protons
Mass number – number of
protons and neutrons
Isotopes – variant forms of the
same element that differ in the
number of neutrons
Atomic weight – average
mass numbers of all isotopic
forms
Electron orbitals – volumes of
space surrounding the atomic
nucleus where electrons are
likely to be found
Shell
Hydrogen
Shell 2
Shell 1
Carbon
Orbitals
(a)
Nucleus
1 proton
1 electron
Hydrogen
Shells
Nucleus
proton
Nucleus
(b)
6 protons
6 neutrons
6 electrons
Carbon
neutron
electron
5
Biologically Important Atoms
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Chemical symbol
H
HYDROGEN
N
Atomic number
1
7
NITROGEN
O
Chemical name
8
OXYGEN
7p
1p
Number
Of e– in
Each
Energy
level
Mg
12
C
MAGNESIUM
6
2•5
H
1
8p
N
CARBON
H
He
P
SO
QN
AT. MASS 14.00
AT. MASS 1.00
12p
Li
Na
2•6
6p
Be
11
Na
11p
Mg
K
Ca
Rb
Sr
2•8•2
2•4
AT. MASS 24.30
AT. MASS 12.01
Sc
Ti
Cr
N
O
F
Ne
AT. MASS 16.00
Al
Si
P
S
Cl
Ar
Cl
Mn
Fe
Co
Ni
Tc
Ru
Rh
Pd
Re
Os
Ir
Pt
Cu
17
CHLORINE
Zn
Ga
Gs
As
Se
Br
Kr
17p
Na
2•8•1
Ca
AT. MASS 22.99
CALCIUM
Cs
K
V
C
c
Mg
SODIUM
B
20
15
PHOSPHORUS
Ba
Fr
16
Cl
SULFUR
2•8•7
Ra
15p
20p
Ca
19p
S
AT. MASS 35.45
19
POTASSIUM
P
16p
S
P
2•8•8•2
2•8•5
AT. MASS 40.08
AT. MASS 30.97
2•8•6
AT. MASS 32.06
K
2•8•8•1
AT. MASS 39.10
6
Concept Check:
If two atoms have the same number of protons and electrons
but different numbers of neutrons, they would be
A. Different elements
B. Isotopes of the same element
C. Ions of the same element
D. Orbitals of the same element
7
Bonds and Molecules
• Molecule - a chemical substance that results from
the combination of two or more atoms
• Compounds - molecules that are combinations of
two or more different elements
• Formula/Mass weight - sum of all of the atomic
masses of the atoms a molecule contains
• Chemical bonds - when 2 or more atoms share,
donate, or accept electrons to form molecules and
compounds
– 3 types: covalent, ionic, and hydrogen
8
3 Types of Chemical Bonds
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1. Covalent bonds –
electrons are shared
among atoms
–
–
Polar covalent bonds
– unequal sharing
Nonpolar covalent
bonds – equal sharing
Covalent Bonds
Single
Double
8
Covalent Bonds
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+
H
e–
H
e–
H2
e–
1p+
1p
1p+
e–
H H
1p+
Single bond
Hydrogen atom
+
Hydrogen atom
Hydrogen molecule
H
8p+
8n
1p+
H C H
H
8p+
8n
H
1p+
Molecular oxygen (O2)
O O
Double bond
C
6p+
6n
1p+
H
H
H
Methane (CH4)
1p+
10
Polarity
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(–)
(–)
O
H
8p+
H
O
1p+
(+)
(a)
1p+
H
H
(+)
(+)
(+)
(b)
11
3 Types of Chemical Bonds
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2. Ionic bonds –
electrons are
transferred to one
atom forming
positively charged
cations and
negatively charged
anions
Ionic Bond
(+)
(–)
12
Ionic Bonding
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
2
1
Na
11p+
17p+
12n
18n
Cl
1
2
NaCl crystals
(a)
(b)
Sodium atom (Na)
Na Cl
Chlorine atom (Cl)
[Na]+ [Cl]–
Na
1
Sodium
1
Na
Cl
2
Chloride
Na
2
Cl
1
Na
1
Cl 2
Na
(c)
1
© Kathy Park Talaro
(d)
1
11p
1
Cl
2
Cl
2
Cl
2
H
Na
Na
1
1
Cl
2
1
1
H
2
1
O
2
2
Cl
Na
Cl
1
2
2
17p
Sodium ion (Na1)
Chlorine atom (Cl2)
(cation)
(anion)
2
13
3 Types of Chemical Bonds
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3. Hydrogen bonds – weak
bonds between hydrogen
and other atoms
Hydrogen Bond
Molecule A
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H
H
H
1
Water molecule
1
(+)
O
2
Hydrogen bonds
1
(–)
H
O
or
1
1
H
O
H
H
H
O
N
O
1
H
H
O
H
1
1
Molecule B
14
14
Concept Check:
Molecules where atoms share electrons contain
A. Covalent Bonds
B. Ionic Bonds
C. Hydrogen Bonds
15
Oxidation-Reduction Reactions
Energy exchange in cells is a result of the movement
of electrons from one molecule to another.
Oxidation – the loss of electrons
Reduction – the gaining of electrons
Redox reactions
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1
Na
28 1
Reducing agent
gives up electrons.
Cl
28 7
Oxidizing agent
accepts electrons.
Na
28
Oxidized cation
2
Cl
28 8
Reduced anion
16
Chemical Shorthand
• Reactants - molecules starting a reaction
• Products - substances left by a reaction
• Synthesis reaction - the reactants bond together in a
manner that produces an entirely new molecule
S + O2
SO2
• Decomposition reaction - the bonds on a single reactant
molecule are broken to release two or more products
2H2O2
2H2O + O2
• Exchange reaction - the reactants trade portions between
each other and release products that are combinations of
the two
HCl + NaOH
NaCl + H2O
17
Solutions
Solution – a mixture of one or more substances called
solutes, dispersed in a dissolving medium called a
solvent
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2
1
1
2
NaCl crystals
-
Solutes – Na+ & Cl
Na
1
Na
Cl
Na
2
Cl
1
Na
1
Cl 2
Na
1
1
Cl
2
Cl
2
Cl
2
Cl
2
1
1
1
H
O
Na
Cl
Solvent – H2O
2
2
Cl
2
1
H
Na
Na
1
1
2
1
11p
2
17p
Sodium ion (Na1)
(cation)
Chlorine atom (Cl2)
(anion)
2
18
Aqueous Solutions
• Hydrophilic molecules - dissolve in water
• Hydrophobic molecules - repel water
• Amphipathic molecules - have both hydrophilic
and hydrophobic properties
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Hydrogen
Oxygen
Water molecules
-
+
+
+
+
+
-
+
+
+
-
+
+
+
+
-
-
Na
+
-
+
+
+
-
+
+
-
-
+
+
+
+
+
+
-
+
+
-
+ +
+
-
+
-
+
+
+
+
+
+
+
+
+
-
+
- +
-
+
+
+
+
+
-
+
Cl
+
+
+
+
-
-
-
+
+
+
+
-
+
+
+
+
-
+
+
-
-
19
Acidity, Alkalinity, and the pH Scale
• Ionization of H2O releases hydrogen ions [H+]
and hydroxyl ions [OH ]
• pH scale – ranges from 0 to 14, expresses the
concentration of H+ ions
• pH is the negative logarithm of the concentration of H+
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pH
0
1
2
3
Acidic
4
[H +]
Increasing
acidity
5
6
7
Neutral
8
9
10
[OH –]
11
12
13
14
Basic
(alkaline)
Increasing
basicity
20
pH and Ion Concentration
21
Concept Check:
If solution A has a pH of 2 and solution B has a pH of 4,
which of the following is true?
A. Solution A has 2 times more H+ ions than solution B
B. Solution B has 2 times more H+ ions than solution A
C. Solution A has 10 times more H+ ions than solution B
D. Solution B has 10 times more H+ ions than solution A
E. Solution A has 100 times more H+ ions than solution B
22
The Chemistry of Carbon and
Organic Compounds
• Organic chemicals – compounds containing
carbon bonded to hydrogens
• Carbon is the fundamental element of life
– Contains 4 atoms in its outer orbital
– Can form single, double, or triple covalent bonds
– Can form linear, branched, or ringed molecules
23
The Versatility of Bonding in Carbon
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Linear
C
C
H
C 1
H
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C H
Branched
C
O
C 1
O
C
O
C
C
C
C
N
C 1
N
C N
C
C
C 1
C
C C
C
Ringed
C
C
C
C
C 1
C
C
C
C
C
C
C
C
C
C
C
C
C
C
(a)
N
C 1
N
C
C
N
C
(b)
C
24
Functional Groups of Organic
Compounds
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• Accessory molecules
that bind to organic
compounds
Representative Functional Groups and
Organic Compounds That Contain Them
TABLE 2.3
Formula of
Functional Group
Name
Can Be Found in
R*
Hydroxyl
Alcohols,
carbohydrates
Carboxyl
Fatty acids, proteins,
organic acids
Amino
Proteins, nucleic acids
Ester
Lipids
Sulfhydryl
Cysteine (amino acid),
proteins
Carbonyl,
terminal end
Aldehydes,
polysaccharides
Carbonyl,
internal
Ketones,
polysaccharides
Phosphate
DNA, RNA, ATP
O
H
O
R
C
OH
H
• Confer unique
reactive properties on
the whole molecule
R
C
NH2
H
O
R
C
O
R
H
R
C
SH
H
O
R
C
H
O
R
C
C
O
R
O
P
OH
OH
25
Macromolecules
• Biochemicals are organic compounds produced
by living things
• Macromolecules: large compounds assembled
from smaller subunits
– Monomer: a repeating subunit
– Polymer: a chain of monomers
• 4 Biological Macromolecules: Carbohydrates,
Lipids, Proteins, Nucleic Acids
26
Biological Macromolecules
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27
Carbohydrates
• Sugars and polysaccharides
• General formula (CH2O)n
• Aldehydes and ketones
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
H
Aldehyde group
O
H
C1
C1
6
H
C2
OH
CH2OH
HO
C3
H
H
H
C4
OH
H
C5
OH
H
C6
H
O
5
H
H
O
H
4
1
HO OH
OH
H
3
H
H
2
OH
C2 OH
HO
C3 H
HO
C4 H
OH
H
6
CH2OH
O
5
H
HO
H
4
H
H
H
C5 OH
C6 OH
1
OH
3
H
H
Glucose
H OH
2
OH
C1 O
C2
HO
Ketone group
O
C3 H
H
C4 OH
H
C5 OH
H
H
C6 OH
O
6
HOCH2
OH
5
H
2
H
4
OH
2OH
HO CH
1
3
H
H
Galactose
Fructose
28
Carbohydrates
• Saccharide: simple carbohydrate
– Monosaccharide: 3-7 carbons
– Disaccharide: two monosaccharides
– Polysaccharide: five or more monosaccharides
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O
O
O
O
Monosaccharide
O
Disaccharide
O
O
O
O
O
CH2
O
CH 2
O
O
O
Polysaccharide
29
Carbohydrates
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
• Subunits linked by
glycosidic bonds
H2O
O
C
C
H OH
C 1
C
OH H
C
C
O
C
C
O H
C
C
C
C
O
C
H C
O
C
C
C
(a)
6
• Dehydration
synthesis: loss of
water in a
polymerization
reaction
C
C
C
H
C4
HO
6
CH2OH
CH2OH
O
C
O
C
5
5
H
H
H
H
H
1C 1 C 4
1C
H
OH
O
H
OH
OH HO
2
2
3
3
C
C
C
C
H
OH
H
OH
Glucose
6
CH2OH
C
O
5
H
H
H
H
1C
C4
C4
OH
H
O
HO
2
3
C
C
H
OH
Glucose
1
6
CH2OH
O
C
5
H
OH
H
2
3
C
C
H
1C
1
H2O
1
H2O
CH2OH
O
C
5
OH
H
1(b ) C 1
OH
H
H
3
2
C
C
H
OH
H2O
H
OH
OH
Maltose
(b)
6
CH2OH
C
O
5
H
H
C4
OH
HO
3
C
H
6
CH2OH
O
C
5
H
H
H
1C 1
C4
H
OH
HO
2
OH
3
C
C
H
OH
Glucose
6
CH2OH O
C5
H
H
4
C
OH
1
OH
C
OH
CH OH
3
C 1 2
H
2
H
1C
2
H
C
OH O
6
CH2OH O
C5
H
H
4
C
OH
3
2C
OH
2OH
C CH
1
H
Sucrose
Fructose
(c)
6
CH2OH
O
C
5
H
H
HO
H
1C 1
C4
C4
OH
H
CH HO
H
3
2
C
C
H
OH
(d)
Galactose
1
6
CH2OH
O
C
5
H
H
1C
OH
H
OH
3
2
C
C
H
OH
Glucose
6
CH2OH
O
C
5
H
HO
H
1(b ) C O C 4
C4
OH
H
H
H
3
2
C
C
H
OH
Lactose
6
30
Carbohydrates
• Functions – cell structure, adhesion, and
metabolism
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6
CH2OH
H
OH
CH2OH
H
OH
O
O
H
H
H H
O 4 OH H 1 b
O 4 OH H 1Hb
4
1 b
4H
1 b
OH
H
H
OH
H
H
O
O
O
H H
H H
O
O
H
OH
CH2OH
H
OH
CH2OH
6
6
CH2OH
CH2OH
CH2OH
5
5
5
O
O
O
H H H
H H H
H
H H
4
1 a
4
1 a
4
1 a
O
O
O
O
OH H
OH H
OH H
3
H
2
OH
3
H
2
OH
3
H
2
OH
6
CH2OH
5
O
H
H H
4
1
OH H
Branch O
Branch
2
3
point
H O O
H 6 C OH
5
O
H
H H
4
1
O
OH H
H
bonds
3
H
(a) Cellulose
(b) Starch
2
OH
31
Lipids
• Long or complex, hydrophobic, C - H chains
• Triglycerides, phospholipids in membranes,
steroids like cholesterol
• Functions
– Triglycerides – energy storage
– Phospholipid – major cell membrane component
– Steroids – cell membrane component
32
Triglycerides: 3 fatty acids bound to glycerol
• Triglycerides are used for energy storage
• Could be saturated or unsaturated
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Fatty acids
1
Triglycerides
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
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
O
C
HO
H
Palmitic acid, a saturated fatty acid
2
H
H
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
C
H
H
H
H
H
H
H
H
H
O
C
H
HO
H
H
Linolenic acid, an unsaturated fatty acid
33
Phospholipids: glycerol with 2 fatty
acids and a phosphate group
• Bilayers of phospholipids form membranes
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Variable alcohol group
Phosphate
R
O
O P O2
O
HCH H
HC
CH
Charged
head
Polar lipid molecule
Glycerol
Polar head
Nonpolar
tails
O
O
O C O C
HCH HCH
HCH HCH
Tail
Double
bond
Creates
a kink.
HCH HCH
HCH HCH
HCH HCH
HCH HCH
HCH HCH
HC
HCH
HCH
HCH
HCH
HCH
Water
1 Phospholipids in single layer
HCH
HCH
HCH
HCH
HCH
Water
Water
H
Fatty acids
(a)
2 Phospholipid bilayer
(b)
34
Membrane Lipids
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Glycolipid
Phospholipids
• Cholesterol is
inserted into the
phospholipid bilayer
Cell
membrane
Protein
Site for
ester bond
with a fatty
acid
Cholesterol
Cholesterol
HO
H C
Globular protein
CH2
CH2 H2C
C
C
CH3
H2
CH
HC C
CH2–CH H2C
CH
CH3
C
HC
CH2–C
H2
CH–CH3
CH2
CH2
CH2
CH
CH3 CH3
35
Concept Check:
Triglycerides that have double bonds in their fatty acids are
best described as
A. Saturated
B. Unsaturated
C. Phospholipids
D. Cholesterol
36
Proteins
•
•
•
•
•
•
Predominant molecules in cells
Monomer – amino acids – 20 essential AA’s
Polymer – peptide, polypeptide, protein
Subunits linked by peptide bonds
Fold into very specific 3-D shapes
Functions – support, enzymes, transport,
defense, movement
37
Amino Acids
• Amino acids are
the monomers that
make up a protein
polymer
38
Formation of a Peptide Bond
• Amino acids are attached through peptide bonds
to form proteins
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Bond forming
H
H
N
H
H
N
H
O
C
N
C
R1
OH
H
O
C
R1
R2
H
C
H
H
C
C
H
H
H
C
N
O
H
R2
N
OH
C
N
O
C
H
C
R3
C
N
H
N
OH
H
R4
O
R4
H
C
R3
H
H
O
C
H
C
H
OH
C
O
H
+ 3H2O
C
O
39
Protein Structure
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
• Primary
Structure
• Secondary
Structure
• Tertiary
Structure
Amino acids
1 The primary structure is a series of
amino acids bound in a chain.
Amino acids display small charged
functional groups (red symbols).
2 The secondary structure
develops when CO – and NH –
groups on adjacent amino
acids form hydrogen bonds.
This action folds the chain
into local configurations called
the a helix and b -pleated
sheet. Most proteins have
both types of secondary
structures.
Primary structure
a helix
b-pleated sheet
N
N H
O C
C
C
C O
Secondary structure
N
H N
C O
Detail of hydrogen bond
Disulfide bond
3 The tertiary structure forms when
portions of the secondary structure
further interact by forming covalent
disulfide bonds and additional
interactions. From this emerges a
stable three-dimensional molecule.
Depending on the protein, this may be
the final functional state.
S S
Tertiary structure
• Quaternary
Structure
O C
Projected 3-dimensional
shape (note grooves and
projections)
4 The quaternary structure exists only in
proteins that consist of more than one
polypeptide chain. Shown here is a
model of the cholera toxin, composed
of five separate polypeptides, each
one shown in a different color.
Image courtesy RCSB Protein Data Bank, www.pdp.org
Quaternary structure
40
Nucleic Acids
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• DNA and RNA
• Nucleotide monomer
• DNA – deoxyribonucleic
acid
– A,T,C,G – nitrogen bases
– Double helix
– Function – hereditary
material
• RNA – ribonucleic acid
– A,U,C,G – nitrogen bases
– Function – organize protein
synthesis
N base
Pentose sugar
Phosphate
(a) A nucleotide, composed of a phosphate, a pentose
sugar, and a nitrogen base (either A,T,C,G, or U) is
the monomer of both DNA and RNA.
Backbone
Backbone
P
DNA
D
A
T
U
D
P
P
RNA
R
P
D
C
G
A
D
P
P
R
P
D
G
C
C
D
P
P
R
P
D
T
A
G
D
P
P
R
P
D
A
T
C
D
P
P
R
P
D
C
G
D
P
P
A
R
P
H bonds
(b) In DNA, the polymer is composed of
alternating deoxyribose (D) and
phosphate (P) with nitrogen bases (A,T,C,G)
attached to the deoxyribose. DNA almost
always exists in pairs of strands, oriented
so that the bases are paired across the
central axis of the molecule.
(c) In RNA, the polymer
is composed of
alternating ribose (R)
and phosphate (P)
attached to nitrogen
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bases (A,U,C,G), but
it is usually a single strand.
Nucleotide Components
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
HOCH2 O
• DNA Nucleotides:
– Deoxyribose
– C, G, A or T
H
H
HOCH2 O
OH
H
H
H
H
H
H
OH H
OH OH
Deoxyribose
Ribose
(a) Pentose sugars
H
H
N
O
N
• RNA Nucleotides:
OH
N
H
N
N
H
H
N
– Ribose
– C, G, A or U
N
N
H
H
H
Guanine (G)
(b) Purine bases
H
O
H
N
H
H3C
O
H
H
H
N
N
N
H
Adenine (A)
H
H
N
N
O
H
N
N
O
H
N
H
H
H
Thymine (T)
Cytosine (C)
Uracil (U)
(c) Pyrimidine bases
O
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Double Helix of DNA
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
• DNA is formed by
two very long
polynucleotide
strands linked along
their length by
hydrogen bonds
Backbone
strands
Base pairs
O
O
O
T
D
A
D
Hydrogen
P
O bonds
O
O
P
C
D
G
O
D
O
P
O
O
P
O
D
T
A
D
O
P
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DNA Passing on the Genetic
Message
• Each strand is copied
• Replication is guided
by base pairing
• End result is two
separate double
strands
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Cells
Events in Cell Division
Events in DNA Replication
A
T
C
G
A
T
G
C
H-bonding severed
New
bases
A
T
G
C
Two single strands
T
C
G
A
T
G
C
Two double strands
A
T
A
T
C
G
C
G
A
T
A
T
G
C
G
C
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ATP: The Energy Molecule of Cells
• Adenosine triphosphate
– Nucleotide - adenine, ribose, three phosphates
• Function - transfer and storage of energy
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
NH2
N
7
5
9
N
4 3
N
8
O
–O
P
O–
O
O
O
P O
P
O–
O–
O
6
1N
2
CH2 O
OH OH
Adenosine
Adenosine diphosphate (ADP)
Adenosine triphosphate (ATP)
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Concept Check:
Which of the following is TRUE about RNA?
A. It is a double stranded molecule
B. It contains the sugar deoxyribose
C. It contains the nitrogenous base Uracil
D. It holds the genetic information
E. All of the above are true
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