General Microbiology

Chemistry
 Chemical Formulas and Reactions
Reactants—molecules that participate in reactions
 Shown to the Left of the arrow
Products—molecules formed by reactions
 Shown to the Right of the arrow
An overall equation for photosynthesis
 
6 CO2 6 H 2 O C 6 H 12 O6 6 O2
+ → +
carbon   dioxide water glucose   oxygen
The equation is balanced if the same number of each type of atom occurs on
both sides of the arrow.

Molecular formula for glucose 1-2

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 Periodic table
Element - chemical and physical characteristics recur in a predictable
manner

• There are 92 naturally occurring elements

• Atoms are arranged in periods (rows) and groups (columns)

Atomic Symbol
• name of the atom or element
• H for hydrogen, Na for sodium, C for Carbon

Atomic Number (always a whole number, and the smaller of the

2 numbers)
• All atoms of an element have this same number of protons
• Also gives number of electrons if an atom is electrically neutral

Atomic Mass (Always the larger of the 2 numbers)

• Mass number is equal to sum of protons and neutrons
• electrons have about zero mass
• Atomic weight changes with gravity
 Atomic Structure
Atomic theory states that elements
consist of a single type of atom
• Atoms consist of Subatomic
elements
• Neutrons—neutral charge, found
in nucleus
• Protons—positive charge, found
in nucleus
• Electrons—negative charge,
found outside of nucleus

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 Isotopes
• Some atoms of the same element
differ in the number of neutrons
they possess.
• These atoms are called Isotopes
• All isotopes are unstable
• Highly unstable isotopes will emit
damaging radiation
• In the field of microbiology isotopes
can play several roles
1. Sterilization of equipment and
surfaces (UV & Ionizing radiation)
2. Molecular tagging and tracking
3. Both the cause and treatment for
many cancers
 The Warburg effect
Cancer cells favor anaerobic glycolysis over aerobic
respiration

Detection of cancerous tissue by positron emission

tomography (PET).
The adult male patient had undergone surgical removal of a
primary skin cancer (malignant melanoma).

The image on the left, obtained by whole-body computed

tomography (CT scan), shows the location of the soft
tissues and bones. The central panel is a PET scan after the
patient had ingested 18F-labeled 2-fluoro-2- deoxyglucose
(FdG).

Dark spots indicate regions of high glucose utilization.

When the intensity of the label in the PET scan is translated

into false color (the intensity increases from green to
yellow to red) and the image is superimposed on the CT
scan
CT scan PET scan Merged
 Electron Configuration

Electrons are arranged in shells around nucleus

• Shells closer to nucleus fill first
• Innermost shell can hold up to 2 electrons
• Next shells can hold up to 8 electrons
• Biological molecules are most stable with 8 electrons in outer
shell (“octet rule”)
• Valence electrons are those in outer shell
• Atoms can give up, accept, or share electrons to have 8; this results in an
ion.
 Types of Chemical Bonds
Atoms bond to try and fulfill the octet rule
Types of chemical bonds
• Ionic— attraction between opposite charges
• Covalent—sharing electrons to complete outer shell (can be polar or non polar)

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 Ionic Bonds
An Ionic Bond forms when 2 ions are held together by the
attraction between opposite charges

• Ion: atom that has gained or lost

electron(s)
 Anions gain electron(s) and are negatively
charged
 Cations lose electron(s) and are positively
charged
Ionic compounds are often called Salts or
Electrolytes

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 Covalent Bonds
Covalent bonding occurs when the atoms in question are unwilling to fully release or accept
an electron.
The result is a sharing of electrons

• Some atoms have equal

pulling strength, so they • Some atoms have different pulling
share equally strengths, so the sharing is not equal
• This bond has no charge and • This bond produces temporary and/or
is considered non-polar weak charges and is considered polar

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 Covalent Bonds
Polar covalent bonds result in slight separation of charge
• Important in biological systems
• May result in formation of hydrogen bonds

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 Hydrogen Bonds

Hydrogen bonds: weak bonds

formed when a hydrogen atom in
polar molecule is attracted to
electronegative atom in the same
or another polar molecule
• May be short-lived, but numerous
bonds add strength

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 Water
Polar nature makes water an excellent solvent in which solutes
are dissolved
• Polar and charged substances are
hydrophilic (“water loving”);
dissolve in water

• Non-polar substances are

hydrophobic (“water fearing”);
do not dissolve in water

• Water with dissolved

substances freezes at
lower temperatures

1-13
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 pH of Aqueous Solutions
 pH is a measure of acidity ( concentration)
•  • Water tends to split into ions and ions
• Pure water has equal concentrations ( Molarity) of
and
• Acids increase concentration ; bases decrease it
• Each pH unit (0 to 14) represents ten-fold change in
concentration
• Buffer: a chemical that helps to maintain a relatively
constant pH of solutions
• Base added: buffer releases
• Acid added: buffer combines with

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 Acids and Bases
What constitutes and “acid” and “base”?
Arrhenius:
ACID: Produces H+ in water
BASE: Produces OH- in Water

Bronstead & Lowry:

ACID  Proton Donor
BASE  Proton Acceptor
Lewis:
ACID: Accepts a pair of electrons for sharing
BASE: Donates a pair of electrons for sharing
Organic Chemistry
•Biological
  molecules
• Organic molecules
must contain carbon
and hydrogen.
• Inorganic molecules do
not contain a
combination of carbon
and hydrogen ( and
NaCl).
 Organic Molecules
•Organic
  chemistry
• Biological molecules
• Organic molecules must
contain carbon and
hydrogen.
• Inorganic molecules do
not contain a combination
of carbon and hydrogen
( and NaCl).
 Organic Molecules
•Organic
  chemistry
• Biological molecules
• Organic molecules must
contain carbon and
hydrogen.
• Inorganic molecules do
not contain a combination
of carbon and hydrogen
( and NaCl).
 Carbon
• Total of six electrons—4 in outer shell
• Never engages in ionic bonding; almost
always shares electrons with elements
such as hydrogen, nitrogen, and oxygen
• Most often shares electrons with other
carbon atoms
• Virtually unlimited variety of molecules

Isomers—same number and kinds of atoms in a variety of arrangements

May have different properties
 Carbon
The carbon skeleton and functional
groups
• Size and shape of carbon skeleton or
backbone
• Functional group—specific combination
of bonded atoms that always have the
same chemical properties and always
reacts the same way
• Reactivity of organic molecule largely
dependent on attached functional groups
• Often use R to stand for the rest of the
molecule
 The Biological Molecules of Life

4 categories:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids
The Biological Molecules of Cells
 Classifying Biological Molecules
Monomers - subunits
Polymers - monomers joined together
Conjugates – Monomers or polymers of different types joined
together; below are several conjugates you should know for this
course
• Proteoglycans
• Lipopolysaccharides
• Glycans
Making and Breaking Biological Molecules

Joins monomers to form polymers Breaks polymers into monomers

Removes a water molecule Adds water to a bond

 Carbohydrates
Composed of Carbon, Hydrogen, and Oxygen
Usually in a 1:2:1 ratio: CH2O
Diverse structures and functions
• Energy source
• Energy storage
• Carbon source
• Component of DNA
and RNA
• Structural components of cells
• Cell recognition sites
 Carbohydrates
Monosaccharides
• Single sugar molecule
• Simple sugars
• 3–7 carbon backbone: 𝐂𝟔
•  𝐇 𝟏𝟐𝐎𝟔
• 5-carbon sugars Glucose
• ribose
• deoxyribose
• 6-carbon sugars
• glucose
 Carbohydrates
 Disaccharides: Two monosaccharides bound together
• Common disaccharides
• Sucrose
• Lactose
• Maltose

• Dehydration Synthesis forms covalent bond between hydroxyl groups of monosaccharides

• Hydrolysis breaks bond and yields two monosaccharides

 Carbohydrates

Polysaccharides: Long strings (polymers) of

monosaccharides
• Some function as energy storage molecules.
• Plants store glucose as starch.
• Animals store glucose as glycogen.

• Some are used as structural components

• Cellulose—plant cell walls
• Most abundant of all organic molecules
• Digested only by some microbes
• Chitin—crab, lobster, insect exoskeletons
Carbohydrates in Microbiology
• Survival
 Prevention of desiccation (Drying out)
• Adherence
 Colonization of biological surfaces
 Bacteria / Host interaction
• Resistance to host immunity
 Specific
 Nonspecific
• Cell to Cell recognition
 Infiltration into host
 Carbohydrates in Microbiology
Specific examples that will be discussed later in class:
Polysaccharides in bacteria:

EPS – Extracellular Polysaccharides

CPS – Capsular Polysaccharides

LPS - Lipopolysaccharides

TA – Teichoic Acids

Monosaccharides in microbiology:

Glucose

Glycans

• N- Acetylglucosamine

• N-Acetylmuramic acid
 Lipids
AKA; fats
• All are insoluble in water
• Long nonpolar hydrocarbon
chains
• Relative lack of hydrophilic
functional groups
• In microbiology lipids are
usually considered in the
context of cell membrane
components
 Lipids
Saturated fatty acids
• No double bonds
• Tails pack tightly so solid at
room temperature (fats)

Unsaturated fatty acids

• Double bonds between carbon
atoms
• Kinks prevent tight packing so
liquid at room temperature
(oils)
 Lipids
Triglycerides: most common simple lipids
• Fats or oils composed of three fatty acids linked to glycerol
• Fatty acids: linear chains of bonded C, H atoms with carboxyl group at
one end

Glycerol+3
•  fatty acids →Triglyceride ( fat )
 Lipid Membranes

Phospholipids
• Form the bulk of the plasma
membrane
• One end of the molecule is water-
soluble.
• Polar phosphate head
• Other end of the molecule is not water-
soluble.
• Nonpolar fatty acid tails

Phospholipid structure
 Lipids
Steroids: have characteristic four-ring structure
• Classified as lipids due to water insolubility
• Sterols such as cholesterol have hydroxyl group attached to one
of the rings
• Other steroids include hormones
• Cortisol, progesterone, testosterone

Steroid Ring Sterol (cholesterol)

a) b)
 Proteins
Proteins are the most diverse biological macromolecules in terms of
function
Proteins have many functions including but not limited to:
• Support -
• Metabolism -
• Transport -
• Defense -
• Regulation -
• Recognition -
• Motility -
 Proteins
Proteins are composed of
amino acid monomers
• Central carbon bonded to
• Hydrogen atom
• Amino group
• Carboxyl group
• side chain (R group)*
• 20 different amino acids
• Differ according to R group
 Proteins
Chirality: All amino acids except glycine exist as optical isomers
• Mirror images, but may have different properties
• Most proteins are composed only of L-amino acids
• Bacteria also utilize D-amino acids
 Synthesis and Degradation of Peptides
• Peptide—two or more amino
acids covalently linked

• Peptide bond— bond between 2

amino acids
• Formed by Dehydration Synthesis
• Degraded by Hydrolysis

• Polypeptide—chain of many
amino acids joined by peptide
bonds
 Protein structures
Structural levels

1. Primary: the actual sequence of amino acids

2. Secondary: folding into sheets and helices

3. Tertiary: Secondary sequences interacting with

each other

4. Quaternary: multiple proteins interacting with

each other

Misfolding of these structures is the

cause of a variety of diseases
 Protein Structure
• A protein's function is determined by its three-dimensional shape
• Denaturing - If a protein losses its structure it will lose its function
• Usually due to
• pH
• Temperature
• Structure may or may not recover depending on
• The protein
• What level of organization has been affected
 Nucleic Acids

Polymers of nucleotide
monomers
• DNA - Deoxyribonucleic acid
• Stores genetic information

• RNA - Ribonucleic acid

• Transports genetic information to a
ribosome in order to make
proteins
 Nucleic Acids

Nucleic acids carry genetic information in sequence of nucleotides

Nucleotides are composed of
• Pentose sugar
• Phosphate group
• Nucleobase
 Nucleic Acids
There are 2 general classifications of
Nucleobases
• Purines: adenine (A), guanine (G)
• Two fused rings

• Pyrimidines: cytosine (C), thymine (T),

uracil (U)
• Single ring structure
• Uracil (U) found only in RNA
 Nucleic Acids
Nucleic acids are formed from
linear chains of nucleotides
• Backbone of alternating sugar and
phosphate molecules
• Covalent bond between phosphate
group of one nucleotide and sugar
of the next
• Phosphate group is on the 5' end of
the strand
• Hydroxyl group of sugar is on the 3'
end of the strand
 Nucleic Acids
DNA (Deoxyribonucleic acid) forms
double-stranded helix held together by
hydrogen bonding between nucleobases

Strands of DNA are

1. Antiparallel

2. Complementary

Base-Pairing:
Always 1 Pyrimidine bonding to 1 purine
• A bonds to T
• C bonds to G
 DNA
DNA (Deoxyribonucleic acid) forms double-stranded helix
held together by hydrogen bonding between nucleobases
Strands of DNA are

1. Antiparallel

2. Complementary

Base-Pairing:
Always 1 Pyrimidine
bonding to 1 purine
• A bonds to T
• C bonds to G
 DNA and RNA Structure

Ribonucleic acid (RNA) Several

forms of RNA involved in protein
synthesis
Similar to DNA except:
• RNA is mostly single-stranded
• The sugar is ribose instead of deoxyribose
• Uracil is the nucleobase instead of thymine
• Highly unstable, very short-lived
comparative to DNA

Note: RNA replaces Thymine with Uracil

Comparing Proteins and Nucleic Acids
Relationship between proteins and nucleic acids
• Sequence of bases in DNA determines sequence of amino
acids in a protein.
• Sequence of amino acids determines a protein's structure
and function.
• Small changes in the DNA may cause large changes in a
protein.