Lecture 2 : “Chemistry and Methods”
Chapter 2 Topics
– Fundamental Building Blocks
– Macromolecules
– The Cell
Chapter 3 Topics
– Methods of Culturing Microorganisms
– Microscope
1
Chapter 2
Fundamental Building Blocks
• Atoms
• Elements
• Molecules and compounds
2
Atom - unit of an element
- electron - subatomic, negatively charged
- proton - subatomic, positively charged
- neutron - subatomic, uncharged
Ion - atoms in which the number of protons and electrons is unequal
- cation - less electrons than protons
- anion - more electrons than protons
- atomic number reflects the number of protons
- atomic mass number reflects the number of protons and neutrons
Isotope - atoms with same atomic number but with varying atomic mass
- radioisotopes are unstable isotopes - used in research and medical
applications and in dating fossils and ancient materials
Pure chemical substances composed of atoms with
the same number of protons, are called
Chemical ELEMENTs
All chemical matter consists of elements.
New elements of higher atomic number are discovered
from time to time, usually as products of artificial
nuclear reactions.
Different Types of Atoms
Elements and Their Properties
• Changes in numbers of protons, neutrons, and
electrons in atoms create different elements
Example: radioisotopic decay (“nuclear fission”).
(this is NOT equal to “atoms interacting chemically with one another”)
• Each element has a characteristic atomic
structure and predictable chemical behavior
• Each assigned a distinctive name with an
abbreviated shorthand symbol
• All elements are organized in the periodic table
5
Atoms (elements) consist of protons and neutrons
(resident in a space called nucleus) and electrons
(resident in the shell).
- a shell reflects a period in the periodic system
- a valence shell is the most outer occupied one
(usually not complete)
- a group includes elements of the same valence
8
Fig. 2.1 Models of atomic structure
Electrons within a given shell are not all
equal and the occupy “preferred spaces” in
the shells, also referred to as “Orbitals.”
10
Fig. 2.1 Models of atomic structure
Electron Orbitals and Shells
• An atom can be envisioned as a central nucleus
surrounded by a “cloud” of electrons
• Electrons rotate about the nucleus in pathways
(“preferred spaces”) 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 unique pattern of orbitals
and shells
11
Each element is characterized by a
specific “Electron configuration”:
2 2 6 2 6 2 10 6
1s2 2s2 2p6 3s2 3p6 4s2 4d10 4p6 ……
He Be Ne Mg Ar Ca Zn Kr
13
Figure 2.2
Bonds and Molecules
• Most elements do not exist naturally in pure form
• Molecule - a distinct chemical substance that results
from the combination of two or more atoms (can be two
of the same element, such as O2)
• Compounds - molecules that are combinations of two
or more different elements (such as CO2)
• 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
14
Chemical bonds
• Covalent
• Ionic
• Hydrogen
15
Chemical bonds involve atoms sharing, donating or accepting electrons
16
Fig. 2.3 General representation of three types of bonding
Covalent bonds: shared electron bond
Usually, the number free valences determines the number of
possible covalent bonds.
Carbon tends to form only covalent bonds thereby generating
an organic compound.
CH4, CO2, HCN
The sharing of electrons generates “noble gas electron
configurations” (valences are completely occupied); hence,
stable bonds.
Hydrogen gas, molecular oxygen, and methane are examples of covalent bonding
(atoms sharing electrons).
1s2
1s2 1s2
2s2 2s2
2p2 + 2p2 2p2 + 2p2
18
Fig. 2.4 Examples of molecules with covalent bonding
Polar vs. Nonpolar Molecules
• Some covalent bonds result in a polar
molecule - an unequal distribution of the
electrons (charge); example: H2O.
– Polarity is a significant property of many
large molecules, influences both reactivity
and structure
• An electrically neutral molecule is nonpolar
• Van der Waals forces- weak attractions
between molecules with low levels of polarity
19
Polarity can occur with different types of covalent bonding (ex. H2O)
20
Fig. 2.5 Polar molecule
Ionic Bonds: Electron Transfer Among Atoms
• Electrons transferred completely from one atom to
another, without sharing, results in an ionic bond
(ex. NaCl)
• Molecules 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
21
====>
Ionic bonds: electrostatic attraction
between oppositely charged ions.
Compounds with ionic bonds (ionic
compounds) are usually inorganic and
organized in a lattice.
Sodium chloride (table salt) is an example of ionic bonding
(electron transfer among atoms or redox reaction).
==> -1 ==> 8
p>e p<e
23
Fig. 2.6 Ionic bonding between sodium and chlorine
Ionic bonding molecules breakup (ionization) when dissolved in a solvent
(water), producing separate positive and negative particles.
24
Figure 2.7 Ionization
Hydrogen bonds: interaction of
hydrogen atoms (covalently bound to
oxygen or nitrogen) with weak
opposing electronic charges.
Polarity of the molecule leads to
interaction with other polar molecules
(water).
Hydrogen bonding is the attraction between the
positive hydrogen ion & a negative atom.
An example would be water molecules.
Covalent bond
Fig. 2.8 Hydrogen bonding in water 26
Formulas, Models, and Equations
• Molecular formula - gives atomic symbols
and the number of elements involved in
subscript (H2O, C6H12O6).
• Molecular formulas might not be unique
(i.e., glucose, galactose, and fructose)
• Structural formulas illustrate the number
of the atoms and the number and types of
bonds including individual relationships
between Atoms in a molecule/compound
27
28
Figure 2.9
Chemical Equations
• Balance equations are used to illustrate
chemical reactions
– Reactants- Molecules entering (used in)
a reaction
– Products- the compounds produced by a
reaction
29
Types of Reactions
• Synthesis: reactants bond together to form
an entirely new molecule
– 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
– AB <--> A + B
– 2H2O2 <--> 2H2O + O2
30
• Exchange: The reactants trade places
between each other and release
products that are combinations of the
two
AB + XY <--> AX + BY (reversible reaction)
• Catalysts (metals or Enzymes)-
increase the rate of the reaction (lower
the activation energy)
31
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
– Hydrophilic molecules - attract water to their surface (polar)
– Hydrophobic molecules - repel water (nonpolar)
– Amphipathic (amphiphilic) molecules - have both hydrophilic and
hydrophobic properties
32
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 mass of a compound in
grams
33
34
Figure 2.11
Acidity, Alkalinity, and the pH Scale
• Acidic solutions - when a compound
dissolved in water (acid) releases excess
hydrogen ions (H+)
• Basic solutions- when a compound
releases excess hydroxide ions (OH-)
35
pH scale
• pH scale- measures the acid and base
concentrations of solutions:
– Ranges from 0 (most acidic) to 14 (most basic); pH= 7
is neutral (i.e., [H+] = [OH-])
– pH = -log[H+]
36
37
The pH of an environment (exterior or interior of a cell) is
important for living systems.
38
Fig. 2.12 The pH scale
Neutralization Reactions
• Neutralization reactions- occur in
aqueous solutions containing both acids
and bases
• Give rise to water and other neutral by-
products
• HCl + NaOH <--> H2O + NaCl
39
Molecules
• Can be inorganic and organic molecules.
– Inorganic: C or H is present (ex. CO2, H2)
– Organic: C and H are present (ex. CH3OH)
• Molecules can form complex Compounds
40
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 itself and other atoms
– Most of the chemical reactions and structures of
living things involve organic chemicals
41
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 molecules
• Can form single, double, or triple bonds
• Most often associates with H, O, N, S, and P
42
43
Figure 2.13
Functional Groups of Organic
Compounds
• Special molecular groups or accessory molecules that
covalently or hydrogen-bond to organic compounds are
called functional groups.
• FG help define the chemical class of certain groups of
organic compounds
• FG give organic compounds unique reactive properties
– Reactions of an organic compound can be predicted by
knowing the kind of functional group or groups it carries
44
The carbon in
inorganic and organic
molecules is the
basic fundamental
element of life.
Functional groups (R)
bind to these
carbons.
Table 2.3 Representative
functional groups and
classes of organic compounds 45
• Biochemistry: study of the compounds of life,
their synthesis and degradation
• Biochemicals: organic compounds produced
by (or components of) living things
Biochemicals can be very large and thus called
more specifically: macromolecules.
46
2.2 Macromolecules
• Polysaccharides (Carbohydrates)
• Lipids
• Proteins
• Nucleic acids
Macromolecules (polymers) are the product of condensation
(polymerization) reactions, in which monomers are
polymerized thereby forming water.
47
Carbohydrates
Sugars and Polysaccharides
• Exist in a variety of configurations
– Sugar (saccharide): a simple carbohydrate with a sweet taste
– Monosaccharide usually 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
– Hexoses- six carbons
– Pentoses- five carbons
– Fructose- for fruit
48
Carbohydrates
• Carbohydrates: Sugars and Polysaccharides
Most can be represented by the general formula
(CH2O)n
where n = the number of units of this combination
of atoms
49
Major sugars (monosaccharides) in the cell are glucose, galactose and
fructose. Several sugars bonded together are called polysaccharides.
50
Fig. 2.14 Common classes of carbohydrates
Sugars are bonded by glycosidic bonds. Water is released (condensation,
dehydration) after the bond is formed.
51
Fig. 2.15 Glycosidic bond
Peptidoglycan in bacteria is an example of a polysaccharide.
Poly-cellobiose = cellulose
Starch: (1,4)-bonded (linear) and
Glycogen: (1,6) branching starch
52
Fig. 2.16 Polysaccharides
Lipids:
Fats & Oils, Phospholipids, and Waxes
• Lipids- a variety of substances that are not
soluble in polar solvents
• Building blocks: Alcohol and fatty acids
• Will dissolve in non-polar solvents
• Main groups of lipids:
• Triglycerides (Fats & Oils)
• Phospholipids
• Miscellaneous lipids: Steroids & Waxes
53
Lipids
• Triglycerides (Includes fats and oils) :
A single molecule of the poly-alcohol
glycerol covalently bound to three fatty
acids
54
FGs
55
Figure 2.17
Phospholipids
• Phospholipids - Contain
- glycerol with
- two fatty acids attached to
- a phosphate group on the
third glycerol binding site
• Phospholipids serve as a
major structural component
of cell membranes.
56
Figure 2.18
Miscellaneous Lipids
• Steroids: complex ringed compounds commonly
found in cell membranes and as animal hormones
– Best known: cholesterol
• Waxes: esters formed between a long-chain
alcohol and a saturated fatty acid
57
Cholesterols are associated with cell membranes of some cells. They bind to
the fatty acid of a lipid.
58
Fig. 2.19 Formula for cholesterol.
Proteins
• Proteins are the predominant organic
molecule in cells (58% of dry mass)
• Building blocks (monomers): amino acids
• Proteins consist of a series of amino acids
(ex. Peptides, polypeptides)
• Examples: enzymes, immunoglobulins, etc.
59
Proteins: “Shapers of Life”
• Building blocks- amino acids
– 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
60
Ala
Amino acids vary based Val
on their reactive (R)
groups present.
Cys
Phe
Fig. 2.20 Structural formula of Tyr
selected amino acids 61
Similar
62
Table 2.5 Twenty natural occurring amino acids and their abbreviations
A covalent peptide bond forms between the amino group on one amino acid
and the carboxyl group on another amino acid.
Fig. 2.21 The formation of a peptide bonds in a tetrapeptide 63
Proteins take on a variety of shapes, which enables specific
interactions (function) with other molecules.
N C
64
Fig. 2.22 Stages in the formation of a functioning protein
Nucleic acids
• Deoxy-ribonucleic acid (DNA)
• Ribonucleic acid (RNA)
• DNA contains genetic information which
is captured (transcribed) into RNA
• The information stored in RNA can be
translated into the primary sequence of
proteins
65
Nucleic acids are polymers of monomers called nucleotides.
nucleoside
nucleotide
66
Fig. 2.23 The general structure of nucleic acids
The pentose sugars and nitrogen bases determine whether a
molecule will be DNA or RNA.
Fig. 2.24 The sugars and nitrogen bases that make up DNA and RNA. 67
The DNA
configuration
is a double
helix.
Fig. 2.25 A structural
representation of the
double helix of DNA 68
DNA serves as a
universal
template for the
synthesis
of new DNA,
mRNA,
tRNA and
rRNA.
Fig. 2.26 Simplified
view of DNA
replication in cells. 69
The Cell
• Fundamental components:
– Genetic element
– Membrane
– Ribosome
• Fundamental characteristics
– Reproduction
– Metabolism
– Motility (Response to molecules)
– Protection and Storage (Cell wall or membrane)
– Nutrient transport
70
Chapter 3
Topics
– Methods of Culturing Microorganisms
– Microscope
71
Methods of Culturing
Microorganisms
• Five basic techniques
• Media
• Microbial growth
72
Five basic techniques
1. Isolation
2. Inoculate
3. Incubate
4. Inspection
5. Identification
73
Inoculation and Isolation
• Isolation: separating one species from another
– Separating a single bacterial cell from other cells and
providing it space on a nutrient surface will allow that
cell to grow in to a mound of cells (a colony).
– If formed from a single cell, the colony contains cells
from just that species.
• Inoculation: producing a culture
– Introduce a tiny sample (the inoculum) into a container
with nutrient medium
74
75
Fig. 3.2 Isolation technique
Fig. 3.3 Three basic methods for isolating bacteria. 76
Streak Plate Method
• Streak plate method- small droplet of culture or
sample spread over surface of the medium with an
inoculating loop
– Uses a pattern that thins out the sample and separates the
cells
77
Figure 3.3 a,b
Loop Dilation Method
• Loop dilation, or pour plate, method- sample inoculated
serially in to a series of liquid agar tues to dilute the number
of cells in each successive tubes
– Tubes are then poured in to sterile Petri dishes and allowed to
solidify
78
Figure 3.3 c,d
Spread Plate Method
• Spread plate method- small volume of liquid, diluted
sample pipette on to surface of the medium and
spread around evenly by a sterile spreading tool
79
Figure 3.3 e,f
Media: Providing Nutrients in the
Laboratory
• At least 500 different types
• Contained in test tubes, flasks, or Petri dishes
• Inoculated by loops, needles, pipettes, and swabs
• Aseptic technique necessary
• Classification of media
– Physical state
– Chemical composition
– Functional type
80
81
Classification of Media by Physical
State
• Liquid media: water-based solutions, do not solidify at
temperatures above freezing, flow freely when container is
tilted
– Broths, milks, or infusions
– Growth seen as cloudiness or particulates
• Semisolid media: clotlike consistency at room temperature
– Used to determine motility and to localize reactions at a
specific site
• Solid media: a firm surface on which cells can form discrete
colonies
– Liquefiable and non-liquefiable
– Useful for isolating and culturing bacteria and fungi
82
Liquid media are water-
based solutions that are
generally termed broths,
milks and infusions.
83
Fig. 3.4 Sample liquid media
Semi-solid
media contain a
low percentage
(<1%) of agar,
which can be
used for motility
testing.
84
Fig. 3.5 Sample semisolid media
Solid media contain a high percent (1-5%) of agar, which enables
the formation of discrete colonies.
85
Fig. 3.6 Solid media that are reversible to liquids
Classification of Media by
Chemical Content
• Synthetic media- compositions are
precisely chemically defined
• Complex (nonsynthetic) media- if even
just one component is not chemically
definable
86
Synthetic media contain pure organic and inorganic compounds
that are chemically defined (i.e. known molecular formula).
Table 3.2 Medium
for the growth and
maintenance
of the Green Alga
87
Euglena
Complex or enriched media contain ingredients that are not
chemically defined or pure (i.e. animal extracts).
Fig. 3.7 Examples of
enriched media 88
Classification of Media by
Function
• General purpose media: to grow as broad
a spectrum of microbes as possible
– Usually nonsynthetic
– Contain a mixture of nutrients to support a
variety of microbes
– Examples: nutrient agar and broth, brain-heart
infusion, trypticase soy agar (TSA).
89
Functional types of growth media
• Enriched media
• Selective media
• Differential media
90
Enriched Media
• Enriched media- contain complex
organic substances (for example blood,
serum, growth factors) to support the
growth of fastidious bacteria.
Examples: blood agar, Thayer-Martin
medium (chocolate agar)
91
Selective media enables
one type of bacteria to grow,
while differential media
allows bacteria to show
different reactions
(i.e. colony color).
Fig. 3.8 Comparison of
selective and different Media
with general-purpose media. 92
Examples of
differential media.
Table 3.4
Differential media 93
Mannitol salt agar is a
type of selective
media, and
MacConkey agar is a
type of differential
media.
94
Fig. 3.9 Examples
of media that are
both selective and
differential
95
Miscellaneous Media
• Reducing media- absorbs oxygen or slows its penetration in
the medium; used for growing anaerobes or for determining
oxygen requirements
• Carbohydrate fermentation media- contain sugars that can
be fermented and a pH indicator; useful for identification of
microorganisms
• Transport media- used to maintain and preserve specimens
that need to be held for a period of time
• Assay media- used to test the effectiveness of antibiotics,
disinfectants, antiseptics, etc.
• Enumeration media- used to count the numbers of
organisms in a sample.
96
Examples of miscellaneous media are reducing, fermentation
and transportation media.
Fig. 3.11
Carbohydrate
fermentation
broth 97
Microbial growth
• Incubation
– Varied temperatures, atmospheric states
• Inspection
– Mixed culture
– Pure culture
• Identification
– Microscopic appearance
• Maintenance and disposal
– Stock cultures
– sterilization
98
Microscope
• Magnification
• Resolution
• Optical microscopes
• Electron microscopes
• Stains
99
3.2 The Microscope: Window on an
Invisible Realm
• Two key characteristics of microscopes:
magnification and resolving power
100
A compound microscope is typically used in teaching and
research laboratories.
101
Fig. 3.14 The parts of a student laboratory microscope
Principles of Light Microscopy
• Magnification
– Results when visible light waves pass through a
curved lens
– The light experiences refraction
– An image is formed by the refracted light when an
object is placed a certain distance from the lens and
is illuminated with light
– The image is enlarged to a particular degree- the
power of magnification
• Magnification- occurs in two phases
– Objective lens- forms the real image
– Ocular lens- forms the virtual image
– Total power of magnification- the product of the
power of the objective and the power of the ocular
102
Resolution
• Resolution- the ability to distinguish two adjacent objects or
points from one another
• Also known as resolving power
– Resolving power (RP) = Wavelength of light in nm
2 x Numerical aperture of objective lens
– Shorter wavelengths provide a better resolution
– Numerical aperture- describes the relative efficiency of a lens in
bending light rays
– Oil immersion lenses increase the numerical aperture
103
A specimen is magnified as light passes through the objective and
ocular lens.
Fig. 3.15 The
pathway of light
and the two
Stages in
magnification of a
compound
104
microscope.
Resolution can be increased by using immersion oil.
Figs. 3.17 and 3.18 Workings of an oil immersion lens,and effect of
magnification. 105
Comparison of optical and electron microscopes.
Table 3.6 Comparison of light microscopes and 106
Electron microscopes
Stains
• Positive stains
– Dye binds to the specimen
• Negative stains
– Dye does not bind to the specimen, but
rather around the specimen.
107
108
Figure 3.25
Optical microscopes
• All have a maximum magnification of
2000X
– Bright-field
– Dark-field
– Phase-contrast
– Differential interference
– Fluorescent
– Confocal
109
Summary of optical and electron microscopes.
110
Table 3.5 Comparison of types of microscopy