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Chapter 2
The
Chemistry of
Microbiology
© 2012 Pearson Education Inc.
Lecture prepared by Mindy Miller-Kittrell
North Carolina State University
Atoms
• Matter – anything that takes up space and
has mass
• Atoms – the smallest chemical units of
matter
© 2012 Pearson Education Inc.
Atoms
• Atomic Structure
– Electrons – negatively charged subatomic
particles circling a nucleus
– Nucleus – structure containing neutrons and
protons
– Neutrons – uncharged particles
– Protons – positively charged particles
© 2012 Pearson Education Inc.
Figure 2.1 Bohr model of atomic structure
Electron shells
Nucleus
Proton (p)
Neutron (n0)
Electron (e)
Atoms
• Atomic Structure
– Element – composed of a single type of atom
– Atomic number – equal to the number of
protons in the nucleus
– Atomic mass (atomic weight) – sum of
masses of protons, neutrons, and electrons
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Atoms
• Isotopes
– Atoms of a given element that differ in the
number of neutrons in their nuclei
– Stable isotopes
– Unstable isotopes
– Release energy during radioactive decay
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Figure 2.2 Nuclei of the three naturally occurring isotopes of carbon-overview
Atoms
• Electron Configurations
– Only the electrons of atoms interact, so they
determine atom’s chemical behavior
– Electrons occupy electron shells
– Valence electrons – electrons in outermost
shell that interact with other atoms
© 2012 Pearson Education Inc.
Figure 2.3 Electron configurations-overview
Figure 2.4 Bohr diagrams of the first 20 elements
H
Li Be
Na Mg Periodic table of elements
K Ca
Hydrogen
H
He
B C N O F Ne
Al Si P S Cl Ar
Helium
He
Lithium
Li
Beryllium
Be
Boron
B
Carbon
C
Nitrogen
N
Oxygen
O
Fluorine
F
Neon
Ne
Sodium
Na
Magnesium
Mg
Aluminum
Al
Silicon
Si
Phosphorus
P
Sulfur
S
Chlorine
Cl
Argon
Ar
Potassium
K
Calcium
Ca
Chemical Bonds
• Valence – combining capacity of an atom
– Positive if has electrons to give up
– Negative if has spaces to fill
– Stable when outer electron shells contain eight
electrons
• Chemical Bonds – atoms combine by sharing or
transferring valence electrons
• Molecule – two or more atoms held together by
chemical bonds
• Compound – a molecule composed of more than
one element
© 2012 Pearson Education Inc.
Chemical Bonds
• Covalent Bond – sharing of a pair of
electrons by two atoms
• Electronegativity – attraction of atom for
electrons
– The more electronegative an atom, the
greater the pull its nucleus exerts on
electrons
© 2012 Pearson Education Inc.
Chemical Bonds
• Nonpolar Covalent Bonds
– Shared electrons spend equal amounts of
time around each nucleus
– Atoms with similar electronegativities
– No poles exist
– Carbon atoms form four nonpolar covalent
bonds with other atoms
– Organic compounds contain carbon and
hydrogen atoms
© 2012 Pearson Education Inc.
Figure 2.5a-b Hydrogen and Oxygen
Hydrogen (H)
Hydrogen (H)
Hydrogen molecule (H2)
Oxygen (O)
Oxygen (O)
Oxygen molecule (O2)
Figure 2.5c-d Methane and Formaldehyde
4
Hydrogen (H)
Methane (CH4)
Carbon (C)
or
2
Carbon (C)
Hydrogen (H)
Oxygen (O)
Formaldehyde (CH2O) or
Figure 2.6 Electronegativity values of selected elements
I
III
II
IV
V
VI
Inert
VII gases
He
0.0
H
2.1
Li
1.0
Be
1.5
B
2.0
C
2.5
N
3.0
O
3.5
F
4.0
Ne
0.0
Na
0.9
Mg
1.2
Al
1.5
Si
1.8
P
2.1
S
2.5
Cl
3.0
Ar
0.0
K
0.8
Ca
1.0
Ga
1.6
Ge
1.8
As
2.0
Se
2.4
Br
2.8
Kr
0.0
Sc Ti
1.3 1.5
V Cr Mn
1.6 1.6 1.5
Fe
1.8
Co
1.8
Ni
1.8
Cu
1.9
Zn
1.6
Chemical Bonds
• Polar Covalent Bonds
– Unequal sharing of electrons due to
significantly different electronegativities
– Most important polar covalent bonds involve
hydrogen
– Allow for hydrogen bonding
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Figure 2.7 Polar covalent bonding in a water molecule-overview
Structure of Water Video
• http://www.youtube.com/watch?v=KiZJOTt3D
l0
Ionic vs Covalent Bonds Video
• http://www.youtube.com/watch?v=7DjsD7Hcd
9U
Chemical Bonds
• Ionic Bonds
– Occur when two atoms with vastly different
electronegativities come together
– Atoms have either positive (cation) or
negative (anion) charges
– Cations and anions attract each other and
form ionic bonds (no electrons shared)
– Typically form crystalline ionic compounds
known as salts
© 2012 Pearson Education Inc.
Figure 2.8 The interaction of sodium and chlorine to form an ionic bond
Electron lost
Chlorine atom
Sodium atom
Attraction
of opposite
charges
Sodium ion (Na)
Chlorine ion (Cl)
Formation of
an ionic bond
Sodium chloride (NaCl)
Figure 2.9 Dissociation of NaCI in water
When water surrounds ions in salt crystal,
individual Na and Cl ions break away.
Hydrated sodium ion
Hydrated chlorine ion
Chemical Bonds
• Hydrogen Bonds
– Weak forces that combine with polar covalent bonds
– Electrical attraction between partially charged H+ and
full or partial negative charge on same or different
molecule
– Weaker than covalent bonds but essential for life
– Many help to stabilize 3-D shapes of large molecules
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Figure 2.10 Hydrogen bonds
Hydrogen bond
Cytosine
Guanine
Table 2.2 Characteristics of Chemical Bonds
Chemical Reactions
• The making or breaking of chemical bonds
• Involve reactants and products
• Biochemistry involves chemical reactions of
living things
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Chemical Reactions
• Synthesis Reactions
– Involve the formation of larger, more
complex molecules
– Require energy (endothermic)
– Most common type is dehydration synthesis
– Water molecule formed
– All the synthesis reactions in an organism
are called anabolism
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Figure 2.11a Dehydration synthesis
Small molecule
Small molecule
Dehydration synthesis
Energy
Larger molecule
Chemical Reactions
• Decomposition Reactions
– Break bonds within larger molecules to form smaller
atoms, ions, and molecules
– Release energy (exothermic)
– Most common type is hydrolysis
– Ionic components of water are added to products
– The decomposition reactions in an organism are
called catabolism
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Figure 2.11b Hydrolysis
Large molecule
Hydrolysis
Energy
Small molecule
Small molecule
Chemical Reactions
• Exchange Reactions
– Involve breaking and forming covalent bonds,
and involve endothermic and exothermic steps
– Involve atoms moving from one molecule to
another
– Sum of all chemical reactions in an organism
is called metabolism
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Water, Acids, Bases, and Salts
• Water
– Most abundant substance in organisms
– Most special characteristics due to two polar
covalent bonds
– Cohesive molecules – surface tension
– Excellent solvent
– Remains liquid across wide range of temperatures
– Absorbs significant amounts of energy without
changing temperature
– Participates in many chemical reactions
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Figure 2.12 The cohesiveness of water-overview
Water, Acids, Bases, and Salts
• Acids and Bases
– Dissociated by water into component cations and
anions
– Acid – dissociates into H+ and one or more anions
– Base – binds with H+ when dissolved into water;
some dissociate into cations and OH–
– Metabolism requires balance of acids and bases
– Concentration of H+ in solution expressed using the
pH scale
– Buffers prevent drastic changes in internal pH
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Figure 2.13 Acids and bases-overview
Figure 2.14 The pH scale
Increasing concentration
of H
Extremely
Acidic
Battery acid
Hydrochloric acid
Lemon juice
Beer, vinegar
Wine, tomatoes
Black coffee
Urine, milk
Increasing concentration
of OH
Pure water
Extremely
Basic
Seawater
Baking soda
Milk of magnesia
Household ammonia
Household bleach
Oven cleaner
Sodium hydroxide
Water, Acids, Bases, and Salts
• Salts
– Compounds that dissociate in water into cations
and anions other than H+ and OH–
– Cations and anions of salts are electrolytes
– Create electrical differences between
inside/outside of cell
– Transfer electrons from one location to another
– Form important components of many enzymes
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Organic Macromolecules
• Functional Groups
– Contain carbon and hydrogen atoms
– Functional groups of common arrangements
– Macromolecules – large molecules used by all
organisms
– Lipids
– Carbohydrates
– Proteins
– Nucleic acids
– Monomers – basic building blocks of
macromolecules
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Organic Macromolecules
• Lipids
– Not composed of regular subunits, but are all
hydrophobic
– Four groups
– Fats
– Phospholipids
– Waxes
– Steroids
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Figure 2.15 Fats (triglycerides)-overview
Figure 2.16 Phospholipids-overview
Organic Macromolecules
• Waxes
– Contain one long-chain fatty acid covalently linked
to long-chain alcohol by ester bond
– Completely insoluble in water; lack hydrophilic head
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Figure 2.17 Steroids-overview
Organic Macromolecules
• Carbohydrates
– Organic molecules composed of carbon, hydrogen,
and oxygen (CH2O)n
– Functions
– Long-term storage of chemical energy
– Ready energy source
– Part of backbones of nucleic acids
– Converted to amino acids
– Form cell wall
– Involved in intracellular interactions between animal
cells
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Organic Macromolecules
• Carbohydrates
– Types
– Monosaccharides
– Disaccharides
– Polysaccharides
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Figure 2.18 Monosaccharides-overview
Figure 2.19 Disaccharides-overview
Figure 2.20 Polysaccharides-overview
Organic Macromolecules
• Proteins
– Mostly composed of carbon, hydrogen, oxygen,
nitrogen, and sulfur
– Functions
– Structure
– Enzymatic catalysis
– Regulation
– Transportation
– Defense and offense
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Organic Macromolecules
• Amino Acids
– The monomers that make up proteins
– Most organisms use 21 amino acids in the synthesis
of proteins
– Side groups affect how amino acids interact and how
a protein interacts with other molecules
– A covalent bond (peptide bond) is formed between
amino acids by dehydration synthesis reaction
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Figure 2.21 Amino acids-overview
Figure 2.22 Stereoisomers
Mirror
L-Serine
Left
(Ser)
D-Serine
(Ser)
Right
Figure 2.23 Linkage of amino acids by peptide bonds
Dehydration
synthesis
Carboxyl Amino
group group
Amino acid 1
Amino acid 2
Peptide bond
Dipeptide
Figure 2.24 Levels of protein structure-overview
Organic Macromolecules
• Nucleic Acids
– DNA and RNA: the genetic material of
organisms
– RNA also acts as enzyme, binds amino
acids, and helps form polypeptides
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Organic Macromolecules
• Nucleic Acids
– Nucleotides and nucleosides
– Nucleotides are monomers that make up nucleic
acids
– Composed of three parts
– Phosphate
– Pentose sugar – deoxyribose or ribose
– One of five cyclic nitrogenous bases
– Nucleosides are nucleotides lacking the
phosphate
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Figure 2.25 Nucleotides-overview
Organic Macromolecules
• Nucleic Acids
– Nucleic acid structure
– Three H bonds form between C and G
– Two H bonds form between T and A in DNA
or between U and A in RNA
– DNA is double stranded in most cells and
viruses
– Two strands are complementary
– Two strands are antiparallel
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Figure 2.26 General nucleic acid structure-overview
Organic Macromolecules
• Nucleic Acids
– Nucleic acid function
– DNA is genetic material of all organisms and
of many viruses
– Carries instructions for synthesis of RNA and
proteins; controls synthesis of all molecules in
an organism
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Organic Macromolecules
• Nucleic Acids
– Adenosine triphosphate (ATP)
– Short-term, recyclable energy supply for cells
– Phosphate-phosphate bonds of ATP are highenergy bonds
© 2012 Pearson Education Inc.
Figure 2.27 ATP
Adenine
Ribose
Adenosine (nucleoside)
Adenosine monophosphate (AMP)
Adenosine diphosphate
Adenosine triphosphate