Microbiology- a clinical approach by Anthony
Strelkauskas et al. 2010
Chapter 2: : Fundamental chemistry for microbiology



An understanding of chemistry is essential to
understand cellular structure and function,
which are paramount for your understanding of
microbiology.
Many of the pathogenic effects of infectious
diseases occur at the molecular level.
To understand the infection process, you need
to understand basic chemistry.
© Charles D. Winters / Science Photo Library

Tissues are organized in the following way:
Atoms
Molecules
Cells
Tissues

Atoms are composed of three types of
particles
◦ Protons
 Located in the core of the atom
 Have a positive charge
 The number of protons in an atom is equal to the
atomic number of the atom.
◦ Neutrons
 Located in the core of the atom
 Neutrons have no charge
 The number of neutrons is usually equal to the
number of protons
 The total number of protons and neutrons equals
the atomic weight of an atom.
◦ Electrons
 Have a negative charge
 Located in shells (orbitals) around the outside of
the core
 In an uncharged atom, the number of electrons
is equal to the number of protons.

Shells occupied by
electrons have a
limited capacity.
◦ First shell can only
hold 2 electrons
◦ Second shell can only
hold 8 electrons
◦ Third shell can hold 18
electrons but needs 8
to be stable



If the electron shell
is not full, it is
unstable.
Atoms with unstable
electron shells can
give or receive
electrons to other
atoms.
This stabilizes the
atom and makes ionic
bonding possible.

Ionic bonds (example: salt, NaCl)
◦ Electrons are donated or received by
atoms
◦ Cations: donated an electron and are
positively charged
◦ Anions received an electron and are
negatively charged
◦ Opposite charges are attracted- 2 ions
form an ionic bond

Covalent bonds (example: water
molecule, methane, CH4)
◦ Electrons are shared in outermost
electron shell
◦ Unequal sharing leads to polarity

Hydrogen bonds (example: water)
◦ Form because of polarity of covalent
bonds
◦ Found between and within molecular
structures, render molecule shape
◦ Affected by temperature and pH


Water may be the most important
component for life because it has
properties very important for
physiological function.
Water has three major
properties:
◦ Solubility
 Dissociation of molecules
 Solvent : water
 Solute: what is dissolved
◦ Reactivity
 Dehydration
 Hydrolysis
◦ Heat capacity
 Ability to absorb and retain heat


Microorganisms can live in acidic or alkaline
environments.
Acidity can be viewed as excessive numbers of
H+ ions.
◦ Lower numbers on the pH scale, acidic is low pH.

Alkalinity can be viewed as excessive numbers
of OH- ions.
◦ Higher numbers on the pH scale, basic is high pH.

A neutral pH is 7.0.


Biological molecules are also referred to as
organic molecules.
There are four major categories of biological
molecules:
◦
◦
◦
◦

Carbohydrates
Lipids
Proteins
Nucleic acids
All four categories of biological molecules use
carbon as their backbone.




All carbohydrates contain carbon, oxygen, and
hydrogen.
Carbohydrates can be viewed as the most easily
used and best source of energy.
Organisms and cells can break down or build up
carbohydrates.
There are three major categories of
carbohydrates:
◦ Monosaccharide – smallest carbohydrate like glucose
 Used to build bigger carbohydrate molecules
◦ Disaccharide – two monosaccharides
◦ Polysaccharide – many monosaccharides like glycogen
Glucose (monosaccharide)
Glycogen (polysaccharide)
Sucrose (disaccharide)


Lipids are a chemically diverse group of
substances that includes fats, phospholipids,
and steroids.
They are relatively insoluble in water which
makes them very useful as elements of
cellular structure.


Some lipids contain more energy than
carbohydrates but are harder to break down.
Fatty acids are a key component of all lipids.

Glycerol + Fatty
acids
◦ Monoglycerol
◦ Diglycerol
◦ Triglycerol
hydrophilic
Phosphate
groups are
attached to
fatty acids
hydrophobic
Membranes
Sugars
are
attached
to fatty
acids




4-ring carbon structures
Very hydrophobic
Cholesterol
Hormones


Made out of amino acids
Assume structure
◦ Primary structure: amino acid sequence
 Dipeptide, polypeptide, protein
◦ Secondary structure: folding due to amino acids and
hydrogen bonds
 Alpha helical or beta sheet
◦ Tertiary structure: folding of the chain itself
 Renders 3-D structure
 Hydrogen bonds and disulfide bridges
 Globular or threadlike
◦ Quaternary structure: joining of multiple polypeptide
chains

Proteins can be denatured.
◦ Factors such as pH and temperature can break
hydrogen bonds.
◦ This damage causes changes in shape.
◦ Changes in shape disrupt function.

Protein functions
◦ Structural
◦ Enzymatic
Type III secretion apparatus


Nucleic acids are
involved with cellular
information and also
function as energy
molecules.
Nucleic acids are
composed of


Nitrogenous base + pentose
sugar + phosphate
There are two types
of nucleic acid
information molecule:
◦ DNA – deoxyribonucleic
acid
◦ RNA – ribonucleic acid
(DNA)
(RNA)

The bases that are used to build nucleic acids:

DNA strands are anti-parallel and form a double helix
The bases point inward

RNA is single stranded and can pair with DNA




The major energy molecule in cells is ATP.
It contains the nitrogenous base adenosine, a
ribose sugar, and a chain of three phosphates
bonded to the sugar.
The bonds between these phosphates are highenergy bonds that when broken yield energy.
◦ ATP

ADP + energy
Energy plus phosphate added can rebuild ATP.
◦ ADP + Pi + energy
ATP



Atoms are composed of protons, neutrons and electrons.
Atoms join together to make molecules, which can join
together to make cells, which can join together to form
tissues.
There are three types of chemical bond: ionic, covalent,
and hydrogen bond.
◦ Ionic bonds form when electrons are donated or accepted.
◦ Covalent bonds form when electrons are shared and are strong
chemical bonds.
◦ Hydrogen bonds form between hydrogen atoms and are the
weakest form of chemical bond.



Biological molecules use carbon atoms as their building
blocks.
There are four types of biological molecule:
carbohydrates, lipids, proteins, and nucleic acids.
ATP is the major energy molecule of the cell.


Which of the following is the type of bond holding Na+ and
Cl- ions together in NaCl?
A. Covalent
B. Ionic
C. Polar covalent
D. None of the above
Which of the following statements is not true?
A. Enzymes are used in a chemical reaction.
B. Enzymes increase the probability that a reaction will
occur.
C. Enzymes are proteins.
D. Enzymes lower the energy of activation of a reaction.
E. None of the above


Which of these molecules make up the plasma membrane
of cells?
A. Nucleic acids
B. Carbohydrates
C. Lipids
D. Water
E. None of the above
Starch and glycogen are made up of
A. Amino acids
B. Lipids
C. Fatty acids
D. Carbohydrates
E. Glycerol