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Chapter 2

The
Chemistryof
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

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Atoms

Atomic Structure
Electrons negatively charged subatomic
particles circling a nucleus
Nucleus structure containing neutrons and
protons
Neutrons uncharged particles
Protons positively charged particles

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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 atoms chemical behavior
Electrons occupy electron shells
Valence electrons electrons in outermost
shell that interact with other atoms

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Figure 2.3 Electron configurations-overview

Figure 2.4 Bohr diagrams of the first 20 elements

H
Li Be
Na Mg
K Ca

Hydrogen
H

Periodic table of elements

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
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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

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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

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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

Hydrogen (H)

Methane (CH4)

Carbon (C)

or

Carbon (C)

Hydrogen (H)

Oxygen (O)

Formaldehyde (CH2O) or

Figure 2.6 Electronegativity values of selected elements

III

II

IV

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 Fe
1.6 1.6 1.5 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

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

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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

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Figure 2.27 ATP

Adenine

Ribose
Adenosine (nucleoside)
Adenosine monophosphate (AMP)
Adenosine diphosphate
Adenosine triphosphate