ZO 211 Week 3 lecture

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Week 3 Lecture
Chapters 6, 7 & 8

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Microbial Nutrition
Essential nutrient: any substance that must be
provided to an organism
Macronutrients: required in relatively large
quantities and play principal roles in cell structure
and metabolism:
• Carbon, hydrogen, and oxygen
Micronutrients: present in much smaller amounts
and are involved in enzyme function and
maintenance of protein structure:
• Also known as trace elements
• Examples: manganese, zinc, nickel

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Chemical Composition of E. coli
Organic Compounds % Dry Weight
Proteins 50
Nucleic Acids–RNA 20
Nucleic Acids–DNA 3
Carbohydrates 10
Lipids 10
Miscellaneous 4
Inorganic Compounds % Dry Weight
Water (–)
All others 3
Elements % Dry Weight
Carbon (C) 50
Oxygen (O) 20
Nitrogen (N) 14
Hydrogen (H) 8
Phosphorus (P) 3
Sulfur (S) 1
Potassium (K) 1
Sodium (Na) 1
Calcium (Ca) 0.5
Magnesium (Mg) 0.5
Chlorine (Cl) 0.5
Iron (Fe) 0.2
Trace metals 0.3

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What Microbes Eat
Heterotroph: an organism that must obtain its
carbon in an organic form
Autotroph: an organism that uses inorganic CO2
as its carbon source:
• Has the capacity to convert CO2 into organic
compounds
• Not nutritionally dependent on other living things
Phototroph: microbe that photosynthesizes
Chemotroph: microbe that gets its energy from
chemical compounds

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Nutritional Categories of Microbes by
Energy and Carbon Source
Category Energy Source Carbon
Source
Example
Autotroph Photoautotroph Sunlight CO2 Photosynthetic organisms, such as
algae, plants, cyanobacteria
Chemoautotroph:
Chemoorganic autotrophs
Organic compounds CO2 Methanogens
Chemoautotroph:
Chemolithoautotrophs
Inorganic compounds
(minerals)
CO2 Thiobacillus, “rock-eating”
bacteria
Heterotroph Photoheterotroph Sunlight Organic Purple and green photosynthetic
bacteria
Chemoheterotroph Metabolic conversion of
the nutrients from
other organisms
Organic Protozoa, fungi, many bacteria,
animals
Chemoheterotroph:
Saprobe
Metabolizing the
organic matter of dead
organisms
Organic Fungi, bacteria (decomposers)
Chemoheterotroph:
Parasite
Utilizing the tissues,
fluids of a live host
Organic Various parasites and pathogens;
can be bacteria, fungi, protozoa,
animals

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Autotrophs and
Their Energy Sources
Photoautotrophs:
• Photosynthetic
• Produce organic molecules using CO2 that can be
used by themselves and by heterotrophs
Chemoautotrophs:
• Chemoorganic autotrophs: use organic compounds
for energy and inorganic compounds as a carbon
source
• Lithoautotrophs: rely totally on inorganic minerals
and require neither sunlight nor organic nutrients

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Heterotrophs and
Their Energy Sources(1)
Chemoheterotrophs:
• Derive both carbon and energy from organic compounds
• Process these molecules through cellular respiration or
fermentation
Saprobes:
• Free-living organisms that feed on organic detritus from
dead organisms
• Decomposers of plant litter, animal matter, and dead
microbes
• Recycle organic nutrients

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Heterotrophs and
Their Energy Sources(2)
Parasites:
• Derive nutrients from the cells or tissues of a living host
• Pathogens: cause damage to tissues or even death
• Range from viruses to helminths
• Ectoparasites: live on the body
• Endoparasites: live in the organs and tissues
• Intracellular parasites: live within cells
• Obligate parasites: unable to grow outside of a living host
• Leprosy bacillus and syphilis spirochete

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Essential Nutrients(1)
Carbon Among the common organic molecules that can satisfy this
requirement are proteins, carbohydrates, lipids, and nucleic acids. In
most cases, these molecules provide several other nutrients as well.
Hydrogen Hydrogen is a major element in all organic and several inorganic
compounds, including water (H2O), salts (Ca[OH]2), and certain
naturally occurring gases (H2S, CH4, and H2). These gases are both used
and produced by microbes. Hydrogen helps cells maintain their pH, is
useful for forming hydrogen bonds between molecules, and also
serves as a source of free energy in respiration.
Oxygen Because oxygen is a major component of organic compounds such as
carbohydrates, lipids, nucleic acids, and proteins, it plays an important
role in the structural and enzymatic functions of the cell. Oxygen is
likewise a common component of inorganic salts such as sulfates,
phosphates, nitrates, and water. Free gaseous oxygen (O2) makes up
20% of the atmosphere.

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Essential Nutrients(1)
Carbon Among the common organic molecules that can satisfy this
requirement are proteins, carbohydrates, lipids, and nucleic acids. In
most cases, these molecules provide several other nutrients as well.
Hydrogen Hydrogen is a major element in all organic and several inorganic
compounds, including water (H2O), salts (Ca[OH]2), and certain
naturally occurring gases (H2S, CH4, and H2). These gases are both used
and produced by microbes. Hydrogen helps cells maintain their pH, is
useful for forming hydrogen bonds between molecules, and also
serves as a source of free energy in respiration.
Oxygen Because oxygen is a major component of organic compounds such as
carbohydrates, lipids, nucleic acids, and proteins, it plays an important
role in the structural and enzymatic functions of the cell. Oxygen is
likewise a common component of inorganic salts such as sulfates,
phosphates, nitrates, and water. Free gaseous oxygen (O2) makes up
20% of the atmosphere.

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Essential Nutrients(2)
Nitrogen The main reservoir of nitrogen is nitrogen gas (N2), which makes up
79% of the earth’s atmosphere. This element is indispensable to the
structure of proteins, DNA, RNA, and ATP. Such compounds are the
primary nitrogen source for heterotrophs, but to be useful, they must
first be degraded into their basic building blocks (proteins into amino
acids; nucleic acids into nucleotides). Some bacteria and algae utilize
inorganic nitrogenous nutrients (NO3
–, NO2
–, or NH3). A small number
of bacteria and archaea can transform N2 into compounds usable by
other organisms through the process of nitrogen fixation. Regardless of
the initial form in which the inorganic nitrogen enters the cell, it must
first be converted to NH3, the only form that can be directly combined
with carbon to synthesize amino acids and other compounds.

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Essential Nutrients(3)
Phosphate The main inorganic source of phosphorus is phosphate (PO4
3–),
derived from phosphoric acid (H3PO4) and found in rocks and
oceanic mineral deposits. Phosphate is a key component of nucleic
acids and is therefore essential to the genetics of cells and viruses.
Because it is also found in ATP, it serves in cellular energy transfers.
Other phosphate-containing compounds are phospholipids in
cytoplasmic membranes and coenzymes such as NAD+.
Sulfur Sulfur is widely distributed throughout the environment in mineral
form. Rocks and sediments (such as gypsum) can contain sulfate
(SO4
2–), sulfides (FeS), hydrogen sulfide gas (H2S), and elemental
sulfur (S). Sulfur is an essential component of some vitamins
(vitamin B1) and the amino acids methionine and cysteine; the latter
help determine shape and structural stability of proteins by forming
unique linkages called disulfide bonds.

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Other Important Nutrients
Potassium (K): essential to protein synthesis and
membrane function
Sodium (Na): important for certain types of cell transport
Calcium (Ca): stabilizer of cell wall and endospores of
bacteria
Magnesium (Mg): component of chlorophyll and a
stabilizer of membranes and ribosomes
Iron (Fe): important component of the cytochrome
proteins of cell respiration
Zinc (Zn): essential regulatory element for eukaryotic
genetics

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Osmosis
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Cell Responses to Osmosis
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Transport Processes in Cells
Examples Description
Energy
Requirements
Passive Simple
diffusion
A fundamental
property of atoms and
molecules that exist in
a state of random
motion
None. Substances
move on a gradient
from higher
concentration to
lower
concentration.
Facilitated
diffusion
Molecule binds to a
specific receptor in
membrane and is
carried to other side.
Molecule-specific.
Goes both directions.
Rate of transport is
limited by the number
of binding sites on
transport proteins.
None. Substances
move on a gradient
from higher
concentration to
lower
concentration.
Active Carrier-
mediated
active
transport
Atoms or molecules
are pumped into or
out of the cell by
specialized receptors.
Driven by ATP or
the proton motive
force

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Endocytosis:
Eating and Drinking by Cells
Endocytosis:
• Cell encloses the substance in its membrane
• Simultaneously forms a vacuole and engulfs the
substance
Phagocytosis:
• Accomplished by amoebas and white blood cells
• Ingest whole cells or large solid matter
Pinocytosis:
• Ingestion of liquids such as oils or molecules in solution

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Psychrophiles
Optimum temperature below 15°C
Capable of growth at 0°C
Obligate with respect to cold and cannot grow
above 20°C
Storage at refrigerator temperature causes them
to grow rather than inhibiting them
Natural habitats of psychrophilic bacteria, fungi,
and algae are lakes, rivers, snowfields, polar ice,
and the deep ocean
Rarely pathogenic

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Psychrotrophs
Grow slowly in the cold but have an optimum
temperature between 15°C and 30°C
Staphylococcus aureus and Listeria
monocytogenes are able to grow at refrigerator
temperatures and cause food-borne illness

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Ecological Groups by
Temperature Range
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Gases
The atmospheric gases that influence microbial
growth are O2 and CO2:
• O2 has the greatest impact on microbial growth
• O2 is an important respiratory gas and a powerful
oxidizing agent
Microbes fall into one of three categories:
• Those that use oxygen and detoxify it
• Those that can neither use oxygen nor detoxify it
• Those that do not use oxygen but can detoxify it

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How Microbes Process Oxygen
As oxygen enters cellular reactions, it is
transformed into several toxic products:
• Singlet oxygen (O): an extremely reactive molecule
that can damage and destroy a cell by the oxidation
of membrane lipids
• Superoxide ion (O2
–): highly reactive
• Hydrogen peroxide (H2O2): toxic to cells and used as
a disinfectant
• Hydroxyl radical (OH–): also highly reactive

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How Microbes Protect Themselves Against
Damage from Oxygen By-products
Most cells have developed enzymes that scavenge and
neutralize reactive oxygen by-products
Two-step process requires two enzymes:
Superoxide ion is converted into hydrogen peroxide by
superoxide dismutase
Hydrogen peroxide is converted into harmless water
and oxygen by catalase

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Oxygen Tolerance Patterns in Microbes(2
TUBE 1. Those organisms that are strict aerobes grow only at the top of the tube.
TUBE 2: Facultative anaerobes grow better where oxygen is present, but may also
grow in anoxic environments.
TUBE 3: Those which are indifferent to oxygen and have a strictly fermentative
type of metabolism grow evenly throughout the medium. We term such an
organism an aerotolerant anaerobe
TUBE 4: Those organisms that require a small amount of oxygen will grow towards
the center of the tube. These are microaerophiles.
TUBE 5: Those organisms that are strict/obligate anaerobes will only grow at the
bottom of the tube.
5
Recall from Week 1 (Selective & Differential Media)

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Carbon Dioxide
Capnophiles: organisms that grow best at a
higher CO2 tension than is normally present in
the atmosphere
Important in the initial isolation of the following
organisms from clinical specimens:
• Neisseria (gonorrhea, meningitis)
• Brucella (undulant fever)
• Streptococcus pneumoniae

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pH

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Osmotic Pressure
Osmophiles: live in habitats with high solute
concentration
Halophiles: prefer high concentration of salt”
• Obligate halophiles: Halobacterium and Halococcus grow
optimally at solutions of 25% NaCl but require at least 9%
NaCl
• Facultative halophiles: remarkably resistant to salt, even
though they do not normally reside in high salt environments
• Staphylococcus aureus can grow on NaCl media ranging from
0.1% to 20%

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Radiation
Phototrophs use visible light rays as an energy
source
Nonphotosynthetic microbes tend to be
damaged by the toxic oxygen products produced
by contact with light
Some microbial species produce yellow
carotenoid pigments to absorb and dismantle
toxic oxygen
Ultraviolet and ionizing radiation can be used in
microbial control

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Pressure
Barophiles:
• Exist under pressures that range from a few times to
over 1,000 times the pressure of the atmosphere
• These bacteria are so strictly adapted to high
pressures that they will rupture when exposed to
normal atmospheric pressure

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Strong Partnerships: Symbioses
Symbiosis: general term to denote a situation in which
two organisms live together in a close partnership
• Symbionts: members of a symbiosis
A. Mutualism
B. Synergism
C. Commensalism
D. Parasitism
E. Antagonism

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Steps in Binary Fission of
Rod-Shaped Bacterium
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Rate of Population Growth
Generation time or doubling time:
• The time required for a complete fission cycle, from
parent cell to two daughter cells
• Generation: increases the population by a factor of
two
• As long as the environment remains favorable, the
doubling effect can continue at a constant rate

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The Mathematics of
Population Growth
The size of a population can be calculated by the
following equation:
Nt = (N)2n
• Nt is the total number of cells in the population; t
denotes “at some point in time”
• Nrepresents the starting number of cells
• The exponent n denotes the generation number
• 2n represents the number of cells in that generation

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Steps in a Viable Plate Count
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Growth Curve in Bacterial Culture
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Turbidity Measurements as
Indicators of Growth
©Kathleen Talaro
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Direct Microscopic Count of Bacteria
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Coulter Counter
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Metabolism and
the Role of Enzymes
Metabolism:
• Pertains to all chemical reactions and physical workings of
the cell
Anabolism:
• Any process that results in synthesis of cell molecules and
structures
• A building and bond-making process that forms larger
macromolecules from smaller ones
• Requires the input of energy
Catabolism:
• Breaks the bonds of larger molecules into smaller molecules
• Releases energy

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Simplified Model of Metabolism
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Enzymes: Catalyzing the Chemical
Reactions of Life
Enzymes are biological catalysts:
• Increase the rate of chemical reactions
• Do not become part of the products
• Are not consumed in the process
• Do not create a reaction

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Conjugated Enzyme Structure
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Enzyme Substrate Reactions
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Two Common Control
Mechanisms for Enzymes
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Patterns of Metabolism
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Three Main Metabolism Pathways
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The Nature of Genetic Material(1)
Genome: sum total of genetic material of an
organism:
• Most of the genome exists in the form of
chromosomes
• Some appear as plasmids or in certain organelles of
eukaryotes (mitochondria and chloroplasts)
• Genome of cells composed entirely of DNA
• Genome of viruses can contain either DNA or RNA

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The Nature of Genetic Material(2)
Chromosome: distinct cellular structure composed of
a neatly packaged DNA molecule
Eukaryotic chromosomes:
• DNA wound around histone proteins
• Located in the nucleus
• Diploid (in pairs) or haploid (single)
• Linear appearance
Bacterial chromosomes:
• DNA condensed into a packet by means of histone-like
proteins
• One, two, or three circular chromosomes

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The Nature of Genetic Material(3)
Three categories of genes:
• Structural genes: code for proteins
• Genes that code for RNA machinery used in protein
production
• Regulatory genes: control gene expression
Genotype: the sum of all gene types; an
organism’s distinctive genetic makeup
Phenotype: the expression of certain traits
(structures or functions)

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Locations and Forms of Genome in
Cells and Viruses
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Some Enzymes Involved in DNA
Replication and Their Functions
Enzyme Function
Helicase Unzipping the DNA helix
Primase Synthesizing an RNA primer
DNA polymerase III Adding bases to the new DNA chain; proofreading
the chain for mistakes
DNA polymerase I Removing primer, closing gaps, repairing
mismatches
Ligase Final binding of nicks in DNA during synthesis and
repair
Topoisomerase I
and II
Supercoiling and untangling

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Flow of Genetic Information in Cells
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Transcription
1. Initiation
2. Elongation
3. Termination
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Genetic Code: Codons of mRNA
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Interpreting DNA Code
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Differences Between Eukaryotic and
Bacterial Transcription and Translation
Characteristic Bacteria Eukaryotes
Start codon Always AUG AUG, but codes for a
different form of
methionine
mRNA Can code for several
genes in a series
Only codes for one protein
Transcription
and translation
Occur simultaneously
in the cytoplasm
Transcription occurs in the
nucleus; translation occurs
in the cytoplasm
Genes Exist as an
uninterrupted set of
triplets coding for a
protein
Contain introns that do not
code for proteins and exons
that do code for proteins.
Introns must be edited out.

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Gene Transfer Methods
Examples of
Mode
Factors Involved Direct or
Indirect*
Examples of Products of
Transferred Genes
Conjugation Donor cell with pilus
Fertility plasmid in donor
Both donor and recipient
alive
Bridge forms between cells
to transfer DNA
Direct Drug resistance; resistance to
metals; toxin production;
enzymes; adherence
molecules; degradation of
toxic substances; uptake of
iron
Transformation Free donor DNA (fragment)
Live; competent recipient
cell
Indirect Polysaccharide capsule;
unlimited with cloning
techniques
Transduction Donor is lysed bacterial cell;
Defective bacteriophage is
carrier of donor DNA;
Live recipient cell of same
species as donor
Indirect Toxins; enzymes for sugar
fermentation; drug resistance
*Direct means the donor and recipient are in contact during exchange;
indirect means they are not.

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Conjugation: Resistance Plasmids
Resistance (R) plasmids or factors:
• Bear genes for resisting antibiotics
• Commonly shared among bacteria through
conjugation
Extremely relevent in Medical/Disease Cycles
• Can confer one or more of the following:
• Resistance to multiple antibiotics
• Resistance to heavy metals
• Synthesizing virulence factors such as toxins, enzymes,

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Causes of Mutations
Spontaneous mutation: a random change in the
DNA arising from errors in replication
Induced mutation: results from exposure to
known mutagens, physical or chemical agents
that disrupt DNA:
• Radiation: UV light, X rays
• Chemicals: nitrous acid

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Categories of Mutations(1)
Point mutation: addition, deletion, or
substitution of bases
Missense mutation:
• Any change in the code that leads to the placement
of a different amino acid
• Can create a faulty, nonfunctional protein
• Can produce a protein that functions differently
• Can cause no significant alteration
Nonsense mutation: changes a normal mutation
into a stop codon

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Categories of Mutations(2)
Silent mutation: alters a base, but does not
change the amino acid, and has no effect
Back-mutation: when a gene that has undergone
a mutation reverses back to its original base
composition
Frameshift mutation:
• One or more bases are inserted or deleted
• Changes the reading frame of the mRNA
• Nearly always results in a nonfunctional protein

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Single Nucleotide Polymorphism
Only a single nucleotide is
altered
Passed on genetically
Identification is critical to
the field of personalized
medicine, customized to a
person’s genetic makeup:
• In thrombophilia (a blood-
clotting disorder), a point
mutation in the gene for a
clotting factor causes an
arginine to become a
glutamine

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Gene Cloning(1)
Involves removal of a selected gene from an animal, plant,
or microorganism and its propagation in a host organism
Donor gene must be excised by restriction endonucleases
and isolated
Gene must be inserted into a vector (usually a plasmid or
a virus)
Vector inserts the gene into the cloning host
Cloning host is usually a bacterium or yeast, which can
replicate the gene and translate it into the desired protein
product

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Synthetic Biology
Creating new biological molecules and organisms from
scratch
In 2010, Craig Venter created a self-replicating bacterial
cell from the four nucleotides of DNA:
• Breakthrough of major proportions, as it was the first time a
living, replicating cell had been synthesized from chemicals
Will revolutionize medical science through:
• Creation of precise chemicals to replace those missing in
disease
• Assembly of customized immune components
• Construction of biological molecules that can target cancerous
cells or pathogenic microbes

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Using Genetic Techniques to
Treat Disease
Gene therapy:
replacing a faulty
gene responsible for
disease with a gene
from a healthy
organism
CRISPR: allows
scientists to cut an
organism’s DNA
where they want to
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