Exam 2 Covers Units 3-5: Microbiology Notes for University Biology

Unit 3 Microbiology Concepts

Culturing Bacteria (14%)

Defined vs. complex media

• Defined media
  . contains precise amounts of known chemical
  components. Allowing researchers to control
  nutrient levels and study specific bacterial
  growth conditions.
  . Complex media
  . Contain ingredients like yeast extract, peptones,
  or animal/plant extracts, which provide a broad
  range of nutrients but are not chemically
  defined. Lack Precise control.

Selective Media

• Specialized growth media designed to favor
  the growth of specific microorganisms while
  inhibiting others. They achieve this by
  incorporating selective agents like
  antibiotics, dyes, or specific nutrients
  that only allow certain bacteria to thrive.
• Examples: MacConkey Agar (Selective for
  gram negative bacteria), A medium
  containing penicillin would be selective
  for antibiotic resistant bacteria.

Differential Media

• Distinguish between different types of
  bacteria based on their biochemical
  properties. Differential media allow for
  multiple types of bacteria to grow,
  highlighting differences using indicators
  like dyes or PH changes.
  Example: Recall MacConkey Agar." Media can be both selective and differential
  . Some media containing both selective and
  differential functions can restrict the growth of
  certain bacteria while also helping differentiate
  the bacteria that do grow based on their
  metabolic traits.
  . Example: MacConkey Agar
  o Selective function: Contains bile salts and
  crystal violet. Inhibiting gram positive,
  allowing only gram-negative bacteria to
  grow.
  o Differential Function: Includes lactose and
  neutral red dye, which helps distinguish
  lactose fermenters (turns pink) from non-
  fermenters. (stays colorless)
  o Flow chart of results

Temperature Requirements for Microorganisms

Microorganisms thrive at a wide range of temperatures; they have
colonized different natural environments and have adapted to extreme
temperatures. Both extreme cold and hot temperatures require
evolutionary adjustments to macromolecules and biological processes.
Psychrophiles grow best in the temperature range of 0-15 ℃ whereas
" psychrotrophs thrive between 4℃ and 25 ℃.
" Mesophiles grow best at moderate temperatures in the range of 20 ℃ to
about 45 ℃. Pathogens are usually mesophiles.
Thermophiles and hyperthemophiles are adapted to life at
temperatures above 50 ℃.
. Adaptations to cold and hot temperatures require changes in the composition of
membrane lipids and proteins.

pH Requirements for Microorganisms

" Bacteria are generally neutrophiles. They grow best at neutral pH close to
7.0.
Acidophiles grow optimally at a pH near 3.0.
Alkaliphiles are organisms that grow optimally between a pH of 8 and
10.5.
Extreme acidophiles and alkaliphiles grow slowly or not at all near neutral
pH.Microorganisms grow best at their optimum growth pH. Growth occurs slowly or not at
all below the minimum growth pH and above the maximum growth pH.

Glucose Metabolism (17%)

Heterotroph vs. Autotroph

• Heterotroph
  Cannot make their own food, must consume organic
  matter from other organisms.
  Examples: Fungi, animals, and most bacteria.
• Autotroph
  " These organisms create their own food using energy
  from sunlight or inorganic reactions.
  . Examples: plants, Algae, and some bacteria.

Respiration and Fermentation

• Aerobic Respiration
  " Uses oxygen as the final electron acceptor in the
  electron transport chain. The most efficient way to
  produce energy, yielding up to 38 ATP molecules per
  glucose in prokaryotes. It occurs in the
  mitochondria in eukaryotes, and involves
  glycolysis, the kreb cycle, and oxidative
  phosphorylation.
• Anaerobic Respiration
  " Like aerobic respiration but does NOT use oxygen.
  Relies on other molecules as electron acceptors.
  (nitrate, and sulfate) Generating fewer ATP
  molecules than Aerobic Resp. But more than
  fermentation.
• Fermentation
  " An anaerobic process that does not use an electron
  transport chain. Much less efficient, producing
  only 2 ATP per glucose molecule. Generates
  byproducts like lactic acid or ethanol, depending
  on the organism. Many bacteria use fermentation
  when oxygen is absent.

Aerobic Respiration Equation

o C6 H12 O6 + 6O2 --> 6CO2 + 6H2 O + ATP
o This shows that glucose (C6 H12 O6) reacts with oxygen
(O2) to produce carbon dioxide (CO2) and water (H2O) and
energy in the form of ATP.

Microbial Oxygen Requirements

• Facultative anaerobes
  " These microbes can switch between aerobic
  respiration and anaerobic processes depending on
  oxygen availability.
  . Example: E. Coli can thrive in both.
• Obligate Anaerobes
  " Oxygen is toxic to these microbes. They rely
  entirely on anaerobic metabolism. They often use
  fermentation or anaerobic respiration with
  alternate electron acceptors like sulfate or
  nitrate.
  · Example: Clostridium botulinum
• Obligate Aerobes
  These organisms MUST use oxygen for survival,
  relying exclusively on aerobic respiration. Without
  oxygen they cannot generate enough ATP to survive.
  Example: Mycobacterium tuberculosis.
  . Electron carriers and the terminal electron acceptors

Connecting Genes to Metabolism

o Genes encode enzymes that catalyze metabolic reactions.
Gene expression regulates metabolic pathways, such as the
lac operon in bacteria which controls lactose metabolism
based on environmental conditions.

Unit 4 Microbiology Concepts

Exoenzymes (9%)

• Also known as extracellular enzymes, help organisms digest
  nutrients externally before absorption.
• Examples
  Proteases: Breaks down protein into amino acids
  Amylases: Digest starch into simple sugars.
  " Lipases: Degrade fats into glycerol and fatty acids.
• Some bacteria use coenzymes as a virulence factor helping
  them invade host tissue. For example, Clostridium species
  produce collagenase, which breaks down connective tissue.
• Biotechnical application: Used in food production, biofuels,
  and textile processing.

Biofilms and Dental Health (9%)

Sugar Polymerization in Biofilms

" Plays a key role in plaque formation and bacterial
adhesion. Streptococcus mutans secretes the enzyme
invertase to break down sucrose to its monomers
glucose and fructose. Glucose is used to make glucan,
aiding in biofilm, and fructose is used to make lactic
acid - lowering PH, causing tooth decay.

Quorum Sensing and Autoinducers

" Quorum sensing is a cell to cell communication system
used by bacteria to coordinate gene expression based
on population density.
" They do this using autoinducers. These are small
molecules that are diffused into the environment as
bacterial density increases. Once a threshold is
reached, autoinducers bind to receptors, triggering
gene expression. Allowing bacteria to coordinate
behaviors such as biofilm and plaque formation.

Fermentation in Oral Bacteria

" Many oral bacteria, such as S. Mutans use fermentation
to metabolize sugars when oxygen is scarce. Producinglactic acid - lowering PH. which contribute to biofilm
stability and bacterial adhesion.

Collagenase as a Virulence Factor

Some bacteria produce collagenase, which help break
down connective tissue. It is considered a virulence
factor since it allows bacteria to penetrate deeper
into the tissue causing disease.

Inhibitors and Enzyme Regulation (4%)

Competitive Inhibition

" The inhibitor binds with the active site, competing
directly with the substrate. Resembles the substrate
in shape but does not undergo a reaction.

Allosteric Inhibition

" The inhibitor binds to a site other than the active
site (the allosteric site), changing the shape of the
enzyme, preventing the substrate from binding
effectively.

Gene Regulation (15%)

Constitutive Gene Expression

" Genes are always "on", there is no regulation.

Lactose Metabolism and Inducible Gene Expression

" The lac operon in lactose metabolism is an example of
inducible gene expression meaning genes are normally
turned off, but "turn on" in the presence of lactose.
Without lactose the repressor protein binds to the
operator, blocking RNA polymerase form transcribing
the operon. With lactose, allolactose binds to the
repressor, causing a shape change, the repressor can't
bind to the operator, which allows RNA polymerase to
transcribe. Genes are "on".

Repressible Gene Expression

" Genes are normally turned on but can be turned off
(repressed) when a specific molecule is present insufficient quantity. The opposite of an inducible
system.
. An example would be trp operon, which controls the
synthesis of amino acid tryptophan.
. Allows bacteria to synthesize tryptophan when it
is scarce and "shut off" production when it is
abundant.
" Energy conserving.

Unit 5 Microbiology Concepts

Horizontal Gene Transfer (25%)

Transformation

" The uptake of free DNA from the environment by a
bacterial cell. This DNA usually comes from dead,
lysed cells that have released their DNA into the
environment and can integrate into the recipient's
genome via homologous recombination, giving it new
traits.
· Think of Frederick Griffith experiment with S.
Pneumoniae.

Conjugation

▪
F plasmid conjugation
. F+ cell contains the F plasmid with genes for
Pilus formation and DNA transfer. It forms a
conjugation pilus (sex pilus) and attaches to an
F- cell (recipient) . A single strand of the F
plasmid is transferred to the F - cell. Both
cells synthesize complementary strands, becoming
F+.
. Only the F plasmid DNA is transferred, no
chromosomal DNA. No gene recombination occurs.
▪
HFR conjugation
. High Frequency Recombination. F plasmid is integrated into chromosome, makes it
an HFR cell.
. Hfr cell forms a pilus and attaches to an F-
cell. It begins transferring DNA from the
chromosomal integration site. A portion of the
chromosomal DNA near the insertion site of the F
plasmid, not just the plasmid enters the
recipient. Usually, the entire chromosome isn't
transferred before the pilus breaks, so the F
plasmid is incomplete. The F- cell remains F- but
may integrate new chromosomal genes by
recombination.

Transposons and Conjugation

" Transposons - "jumping genes"
o
Segments of DNA that can move from one
location to another in the genome between
DNA molecules. Can carry antibiotic
resistance genes and other traits.
· Conjugation
o Transposons can jump onto plasmids; these
plasmids then can be transferred to another
cell via conjugation. This spreads
resistance genes and virulence factors
rapidly.

Bacteriophages - Viruses that Infect Bacteria

o
" Viruses inject their genetic material into host and
hijack the bacterial machinery to reproduce.
" Replication cycles
· Lytic
o
The bacteriophage takes over the cell,
reproduces new phages and destroys the
cell.
o There are five stages in this cycle.
" 1 - attachment - the phage attaches to
the surface of the host.
" 2 - Penetration - The viral DNA enters
the host cell.