Transcript Microbiology: A nd Systems Approach, 2 ed. Chapter 2: The Chemistry of Biology 2.1 Atoms, Bonds, and Molecules: Fundamental Building Blocks  Matter: anything that occupies space and has.

Microbiology: A
nd
Systems Approach, 2
ed.
Chapter 2: The Chemistry of
Biology
2.1 Atoms, Bonds, and Molecules:
Fundamental Building Blocks

Matter: anything that occupies space and
has mass
 Can be liquid, solid, or gaseous state
 Building blocks of matter- atoms
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Subatomic particles of atoms- protons (p+),
neutrons (n0), and electrons (e-)
Protons and neutrons make up the nucleus,
electrons surround the nucleus
Held together by the attraction of positive protons
to negative electrons
Figure 2.1
Different Types of Atoms: Elements
and Their Properties
 Different
numbers of protons, neutrons,
and electrons in atoms create different
elements
 Each element has a characteristic atomic
structure and predictable chemical
behavior
 Each assigned a distinctive name with an
abbreviated shorthand symbol
The Major Elements of Life and Their
Primary Characteristics
 Isotopes-
variant forms of the same
element that differ in the number of
neutrons
 Radioactive isotopes used in research and
medical applications and in dating fossils
and ancient materials
 Electron orbitals and shells
Electron Orbitals and Shells
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An atom can be envisioned as a central nucleus
surrounded by a “cloud” of electrons
Electrons rotate about the nucleus in pathways
called orbitals- volumes of space in which an
electron is likely to be found
Electrons occupy energy shells, from lower-energy
to higher-energy as they move away from the
nucleus
Electrons fill the orbitals and shells in pairs starting
with the shell nearest the nucleus
Each element, then, has a unuiqe pattern of
orbitals and shells
Figure 2.2
Bonds and Molecules
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Most elements do not exist naturally in pure form
Molecule- the smallest particle of matter that can have
independent existence; a distinct chemical substance
that results from one atom of a noble gas (Ne) or the
combination of two or more atoms (can be two atoms
of the same element, such as O2).
Compounds- are combinations of two or more
different elements joined by chemical bonds.
Chemical Bonds- When two or more atoms share,
donate, or accept electrons
Types of bonds formed and to which atoms and
element bonds are determined by the atom’s valence
Figure 2.3
Covalent Bonds and Polarity:
Molecules with Shared Electrons
 Covalent
bonds- between atoms that
share electrons (such as H2).
 The majority of molecules associated with
living things are composed of single and
double covalent bonds between C, H, O,
N, S, and P.
Figure 2.4
Polar vs. Nonpolar Molecules
 Some
covalent bonds result in a polar
molecule- an unequal distribution of
charge (ex. H2O).

Polarity is a significant property of many large
molecules, influencing both reactivity and
structure.
 An
electrically neutral molecule is
nonpolar
 Van der Waals forces- weak attractions
between molecules with low levels of
polarity
Figure 2.5
Ionic Bonds: Electron Transfer Among
Atoms
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Electrons transferred completely from one atom
to another, without sharing, results in an ionic
bond (ex. NaCl)
Crystals with ionic bonds, when dissolved in a
solvent, can separate in to charged particles
called ions in a process called ionization
Cations- positively charged ions
Anions- negatively charged ions
These ionic molecules that dissolve to form ions
are called electrolytes
Figure 2.6
Figure 2.7
Hydrogen Bonding
• Weak bond between
a H covalently
bonded to one
molecule and an O or
N atom on the same
or different molecule
(such as between
water molecules)
Figure 2.8
Chemical Shorthand: Formulas,
Models, and Equations
 Molecular
formula- gives atomic symbols
and the number of atoms of the elements
involved in subscript (H2o, C6H12O6).
 Molecular formulas might not be unique
(glucose, galactose, and fructose, for
example)
 Structural formulas illustrate the
relationships of the atoms and the number
and types of bonds
Figure 2.9
Chemical Equations
 Equations
are used to illustrate chemical
reactions
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Reactants- Molecules entering the reaction
Products- the substances left by a reaction
Types of Reactions
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Synthesis: reactants bond together to form
an entirely new molecule
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A + B  AB
S + O2  SO2
2H2 + O2  2H2O (note that equations must be
balanced)
Decomposition: bonds on a single reactant
molecule are permanently broken to release
two or more product molecules
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AB  A + B
2H2O2  2H2O + O2
Types of Reactions:
 Exchange: The reactants trade places
between each other and release products
that are combinations of the two

AB + XY
AX + BY (reversible reaction)
CATALYSTS
 Catalysts-
increase the rate of the
reaction
 Catalysts lower the energy required to get
reactions started
 Enzymes are biological catalysts
 Most enzymes are proteins, but other
substances, e.g. RNA can occasionally
serve as enzymes
Solutions: Homogeneous Mixtures of
Molecules

Solution- a mixture of one or more solutes
uniformly dispersed in a solvent
 The solute cannot be separated by filtration or
settling
 The rule of solubility- “like dissolves like”
 Water- the most common solvent in natural
systems because of its special characteristics
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Hydrophilic molecules- attract water to their surface
(polar)
Hydrophobic molecules- repel water (nonpolar)
Amphipathic molecules- have both hydrophilic and
hydrophobic properties
Concentration of Solutions
 Concentration-
the amount of solute
dissolved in a certain amount of solvent

In biological solutions, commonly expressed
as molar concentration or molarity (M)
• One mole dissolved in 1 L
• One mole is the molecular weight of the compound
in grams
Figure 2.11
Acidity, Alkalinity, and the pH
Scale

Acidic solutions- when a component
dissolved in water (acid) releases excess
hydrogen ions (H+)
 Basic solutions- when a component releases
excess hydroxide ions (OH-)
 pH scale- measures the acid and base
concentrations of solutions
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Ranges from 0 (most acidic) to 14 (most basic); 7
is neutral
pH = -log[H+]
Figure 2.12
Neutralization Reactions
 Neutralization
reactions- occur in
aqueous solutions containing both acids
and bases
 Give rise to water and other neutral byproducts
 HCl + NaOH  H2O + NaCl
The Chemistry of Carbon and Organic
Compounds
 Inorganic
chemicals- usually do not
contain both C and H (ex. NaCl, CaCO3)
 Organic chemicals- Carbon compounds
with a basic framework of the element
carbon bonded to other atoms

Most of the chemical reactions and structures
of living things involve organic chemicals
Carbon- the Fundamental Element of
Life
 Valence
makes it an ideal atomic building
block
 Forms stable chains containing thousands
of C atoms, with bonding sites available
 Can form linear, branched, or ringed
chains
 Can form single, double, or triple bonds
 Most often associates with H, O, N, S, and
P
Figure 2.13
Functional Groups of Organic
Compounds

Special molecular groups or accessory
molecules that bind to organic compoundsfunctional groups
 Help define the chemical class of certain
groups of organic compounds
 Give organic compounds unique reactive
properties
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Reactions of an organic compound can be
predicted by knowing the kind of functional group
or groups it carries
2.2 Macromolecules: Superstructures
of Life
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Biochemistry- study of the compounds of life
 Biochemicals- organic compounds produced
by (or components of) living things
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Four main families- carbohydrates, lipids,
proteins, and nucleic acids
Often very large, called macromolecules
All macromolecules except for lipids are formed
by polymerization
• Repeating subunits (monomers) are bound in to
chains of various lengths (polymers)
Carbohydrates
 Carbohydrates:
Sugars and
Polysaccharides
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Most can be represented by the general
formula (CH2O)n, where n = the number of
units of this combination of atoms
Figure 2.14
Carbohydrates
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Exist in a variety of configurations
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Sugar (saccharide)- a simple carbohydrate with a
sweet taste
Monosaccharide contains 3-7 carbons
Disaccharide contains two monosaccharides
Polysaccharide contains five or more
monosaccharides
Monosaccharides and disaccharides are specified
by combining a prefix that describes a
characteristic of the sugar with the suffix –ose
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Hexoses- six carbons
Pentoses- five carbons
Fructose- for fruit
The Nature of Carbohydrate
Bonds
Figure 2.15
The Functions of
Polysacharides

Structural support and
protection
 Serve as nutrient and
energy stores
 Cell walls in plants
and many
microscopic algae
from cellulose
Figure 2.16a
Other Important
Polysaccharides
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Include agar,
peptidoglycan,
chitin,
lipopolysaccharide,
glycocalyx, and
glycogen
Figure 2.16b
Lipids: Fats, Phospholipids, and
Waxes
 Lipids-
a variety of substances that are
not soluble in polar substances
 Will dissolve in nonpolar solvents
 Main groups of lipids
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Triglycerides-a single molecule of glycerol
bound to three fatty acids
• Includes fats and oils
Figure 2.17
Phospholipids
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PhospholipidsContain two fatty
acids attached to the
glycerol with a
phosphate group on
the third glycerol
binding site
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Important membrane
molecules
Figure 2.18
Miscellaneous Lipids
 Steroids-
complex ringed compounds
commonly found in cell membranes and
animal hormones
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Best known- cholesterol
• Waxes- esters formed between a longchain alcohol and a saturated fatty acid
Figure 2.19
Proteins: Shapers of Life
 Predominant
organic molecules
 Building blocks- amino acids
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20 different naturally occurring forms
Basic skeleton- a carbon (the α carbon) linked
to an amino group (NH2), a carboxyl group
(COOH), a hydrogen atom (H), and a variable
R group
Peptide bond forms between the amino
group on one amino acid and the carboxyl
group on another.
Figure 2.20
Protein Structure and Diversity
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Primary (1°) structure- the type, number, and
order of amino acids in the chain
 Secondary (2°) structure- when various
functional groups exposed on the outer surface of
the molecule interact by forming hydrogen bonds
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Coiled configuration- α helix
Accordion pattern- β-pleated sheet
Tertiary (3°) structure- created by additional
bonds between functional groups
 Quarternary (4°) structure- more than one
polypeptide forms a large, multiunit protein
Figure 2.21
Protein Shape
 Each
different type of protein develops a
unique shape, so it can only react with
molecules that fit its particular surface
features
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Ex. enzymes and antibodies
Native state- the functional three-dimensional
form of a protein
Denatured- when the protein’s native state
has been disrupted
The Nucleic Acids: A Cell Computer
and Its Programs
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DNA- specially coded genetic program
DNA transfers its program to RNA
Both are polymers of repeating units called nucleotides
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Nucleotides- composed of three smaller units: a nitrogen base,
a pentose sugar, and a phosphate.
The nitrogen base can be one of two forms- a purine (two rings)
or a pyrimidine (one ring)
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Two types of purines: adenine (A) and guanine (G)
Three types of pyrimidines: thymine (T), cytosine (C), and uracil (U)
DNA contains all of the nitrogen bases except uracil
RNA contains all of the nitrogen bases except thymine
The nitrogen base is covalently bonded to ribose in RNA and
deoxyribose in DNA
 Phosphate (PO43-) covalently bonds the sugars in series
Figure 2.22
Figure 2.23
The Double Helix of DNA
 Formed
by two long polynucleotide
strands
 Linked along their length by hydrogen
bonds between complimentary pairs of
nitrogen bases
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Adenine pairs with thymine
Cytosine pairs with guanine
Figure 2.24
RNA: Organizers of Protein Synthesis

Also consists of a long chain of nucleotides
 It is single stranded and contains ribose instead of
deoxyribose anduracil instead of thymine
 Several functional types of RNA formed using the
DNA template
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Messenger RNA (mRNA)- a copy of a gene that
provides the order and type of amino acids in a
protein
Transfer RNA (tRNA)- a carrier that delivers the
correct amino acids for protein assembly
Ribosomal RNA (rRNA)- a major component of
ribosomes
ATP: The Energy Molecule of
Cells
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Adenosine triphosphate (ATP)- a nucleotide
containing adenine, ribose, and three phosphates
High-energy compound that gives off energy when
the bond is broken between the outermost
phosphates
Releases and stores energy for cellular chemical
reactions
When the terminal phosphate bond is broken to
release energy, adenosine diphosphate (ADP) is
formed
ADP can be converted back to ATP when the third
phosphate is restored.
Figure 2.25
2.3 Cells: Where Chemicals Come to
Life
 The
fundamental unit of life- cell
 Fundamental characteristics of cells
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Tend to be spherical, polygonal, cubical, or
cylindrical
Their protoplasm is encased in a cell or
cytoplasmic membrane
Chromosomes containing DNA
Ribosomes for protein synthesis
Eukaryotic and Prokaryotic
Cells
 Eukaryotic
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cells
Found in animals, plants, fungi, and protists
Contain organelles that perform cell functions
(such as the nucleus, Golgi apparatus,
endoplasmic reticulum, vacuoles, and
mitochondria)
 Prokaryotic
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cells
Only found n bacteria and archae
No nucleus or other organelles
 Cell