chapter 6 Flashcards
microorganisms need what
- nutrients (carbon, nitrogen, oxygen, hydrogen, phosphate, sulfur, etc)
- energy sources (sunlight, organic compounds, etc.)
- gases (carbon dioxide, and oxygen)
- proper temperature and pH levels
essential nutrient:
essential nutrient: any substance that must be provided to an organism
micronutrients
macronutrients
micronutrients: present in much smaller amounts and are involved in enzyme function and maintenance of protein structures
- also known as trace elements
- examples: manganese, zinc, nickel
macronutrients: are required in relatively large quantities and play principal roles in cell structure and metabolism: (carbon, hydrogen, oxygen)
inorganic nutrients
- an atom or simple molecule that contains a combination of atoms other than C and H
- found in the earth’s crust, bodies of water, and the atmosphere
- metals and their salts (magnesium sulfate, ferric nitrate, sodium phosphate)
- gases (oxygen, carbon dioxide) and water
organic nutrients
- contain carbon and hydrogen atoms and are usually the products of living things
- simple organic molecules such as methane
- large polymers (carbohydrates, lipids, proteins, nucleic acids)
what microbes eat
1) where they get their carbon
- 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
2) where they get their energy
- phototroph: microbes that photosynthesize
- chemotroph: microbes that get its energy from chemical compounds
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
heterotrophs and their energy sources: parasites
- derive nutrients from the cells or tissues of living hosts
- Pathogens: cause damage to tissues of 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 the living host
- leprosy bacillus and syphilis spirochete
essential nutrients - 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.
essential nutrients - 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.
Carbon is what of the essential nutrients
- it is our backbone
- Carbon likes to be with 4 hydrogens
essential nutrients - 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.
essential nutrients - 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
essential nutrients - 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+.
essential nutrients - 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.
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
How microbes eat: transport mechanisms
Transport of necessary nutrients occurs across the
cytoplasmic membrane, even in organisms with cell walls
* The driving force of transport is atomic and molecular
movement
Diffusion
define diffusion
the phenomenon of molecular movement, in
which atoms or molecules move in a gradient from an area
of higher density or concentration to an area of lower
density or concentration
the movement of water: osmosis
Osmosis: the diffusion of water through a selectively, or differentially, permeable membrane:
* Has passageways that allow free diffusion of water, but block certain other dissolved molecules
* When the membrane is placed between solutions of differing concentrations of solute and the solute cannot pass through the membrane, water will diffuse at a faster
rate from the side that has more water to the side that has less water
* This will continue until the concentration of water is equalized on both sides of the membrane
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 solutions
minimum temperature
- the lowest temperature that permits a microbe’s continued growth and metabolism; below this temperature, its activities stop
maximum temperature
Maximum temperature: the highest temperature at which
growth and metabolism can proceed before proteins are
denatured
optimum temperature
- Optimum temperature: an intermediate between the
minimum and the maximum that promotes the fastest rate
of growth and metabolism
cardinal temperatures
the range of temperatures for the growth of a given microbial species
Thermoduric microbes
Can survive short exposure to high temperatures but are
normally mesophiles
* Common contaminants of heated or pasteurized foods
* Examples are heat-resistant endospore formers such as
Bacillus and Clostridium
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
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
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
Aerobes
- can use gaseous oxygen in their
metabolism and possess the enzymes needed
to process toxic oxygen products - An organism that cannot grow without
oxygen is an obligate aerobe - Examples: Most fungi, protozoa, and many
bacteria, such as Bacillus species and
Mycobacterium tuberculosis
Microaerophiles
- are harmed by normal
atmospheric concentrations of oxygen but
require a small amount of it in metabolism - Examples: Organisms that live in soil or
water or in mammalian hosts, not directly
exposed to atmosphere; Helicobacteri pylori,
Borrelia burgdorferi
facultative anaerobes
- do not require oxygen for
metabolism but use it when
it is present - Examples: Many gram - negative intestinal
bacteria, staphylococci
anaerobes
- lack the metabolic enzyme systems
for using oxygen in respiration - Obligate anaerobes also lack the enzymes
for processing toxic oxygen and die in its
presence - Examples: Many oral bacteria, intestinal
bacteria
aerotolerant anaerobes
- do not utilize oxygen but can survive and grow to a limited extent in its presence
- Not harmed by oxygen, mainly because they
possess alternate mechanisms for breaking
down peroxides and superoxide - Examples: Certain lactobacilli and streptococci,
clostridial species
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 (a genus causing gonorrhea and meningitis)
* Brucella (undulant fever)
* Streptococcus pneumoniae
pH
Defined as the degree of acidity or alkalinity of a solution:
* Expressed by the pH scale, a series of numbers ranging
from 0 to 14
* 7.0 is the pH of pure water
* As the pH value decreases toward 0, the acidity increases
* As the pH value increases toward 14, the alkalinity increases
- The majority of organisms live or grow in habitats between
pH 6 and 8
pH extremes - acidophiles
Acidophiles: organisms that thrive in acidic environments:
* Euglena mutabilis: grows in acid pools between pH 0 and 1
* Thermoplasma: lives in coal piles at a pH of 1 or 2
* Picrophilus: thrives at a pH of 0.7, but can grow at a pH of 0
* Many molds and yeasts tolerate acid and are common spoilage
agents of pickled foods
pH extremes - alkalinophile:
Alkalinophiles: organisms that thrive in alkaline conditions:
* Natronomonas: live in hot pools and soils up to pH 12
* Proteus: can create alkaline conditions to neutralize urine and colonize and infect the urinary system
osmotic pressure
- 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%
osmotic pressure
Define osmophiles:
live in habitats with high solute concentration
osmotic pressure:
Halophiles
prefer the high concentration of “salt”
symbiosis
Symbiosis: general term to denote a situation in which two organisms live together in a close partnership
* Symbionts: members of a symbiosis
the three main types of symbiosis that occur
Mutualism: organisms live in an obligatory but mutually beneficial relationship
* Commensalism: the partner called the commensal receives benefits, while its partner is neither harmed nor benefited
* Parasitism: a relationship in which the host organism provides the parasitic microbe with nutrients and a habitat; host suffers from the relationship
antagonism
an association between free-living species that arises when members of a community compete
associations but not partnerships: Antibiosis
Antibiosis: production of inhibitory compounds such as antibiotics into the surrounding environment that inhibit or destroy another microbe in the same habitat
* The first microbe has a competitive advantage by increasing the space and nutrients available to it.
* Common in the soil where mixed communities compete for space and food
synergism
- An interrelationship between two organisms that benefits them but is not necessary for survival
- Together, the participants cooperate to produce a result that neither could do alone
- Gum disease, dental caries, and some bloodstream infections involve mixed infections that are examples of bacteria interacting synergistically
the study of bacterial growth: binary fission
- One cell becomes two
- Parent cell enlarges
- Duplicates its chromosome
- Starts to pull its cell envelope together to the center of the cell
- Cell wall eventually forms a complete septum
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
length of generation time
The length of the generation time is a measure of the growth
-> rate of an organism:
* Average generation time is 30 to 60 minutes
* Shortest generation times can be 10 to 12 minutes
* Mycobacterium leprae has a generation time of 10 to 30 days
* Environmental bacteria have generation times measured in months
* Most pathogens have relatively short generation times
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”
* N represents the starting number of cells
* The exponent n denotes the generation number
* 2n represents the number of cells in that generation
the population growth curve
- Placing a tiny number of cells into a sterile broth
- Incubating the culture over a period of several hours
- Sampling the broth at regular intervals during incubation
- Plating each sample onto solid media (agar), and
- Counting the number of colonies present on each agar
plate after incubation
define population growth curves
a predicable pattern of a bacterial population growth in a closed system can be measured by
steps in the normal growth curve
- the lag phase
The lag phase is a “flat” period of growth due to:
* Newly inoculated cells that require a period of adjustment,
enlargement, and synthesis
* Cells are not yet multiplying at their maximum rate
* Population of cells is so sparse or dilute that sampling
misses them
stages in the normal growth curve:
Exponential growth (logarithmic or log) phase
Exponential growth (logarithmic or log) phase:
* Growth curve increases geometrically
* Will continue as long as cells have adequate nutrients and the environment is favorable
stages in the normal growth curve
- stationary growth phase
- Cell birth and cell death rates are equal
- Cell division rate is slowing down
- Caused by depleted nutrients and oxygen, plus excretion of organic acids and biochemical pollutants into the growth medium
stages in the normal growth curve
- Death phase
- Cells begin to die at an exponential rate due to the buildup
of wastes - Speed with which death occurs depends on the resistance
of the species and how toxic the conditions are - Slower than the exponential growth phase
stage in the normal growth curve:
viable nonculturable state (VNC)
- Many cells in a culture in the death phase stay alive but
are dormant - Will not grow on culture medium and are missed in colony
counts
the practical importance of the growth curve
The tendency for populations to exhibit phases of rapid growth, slow growth, and death has important implications in
controlling microbes in the environment:
* Microbes in the exponential growth phase are more vulnerable to antimicrobial agents and heat
* Cells in the growth phase are more vulnerable to conditions that disrupt cell metabolism and binary fission
* In general, actively growing cells are more vulnerable to growth, inhibition, and destruction
analyzing population size without culturing: Turbidity
Turbidity/turbidometry:
* A clear nutrient solution becomes turbid, or cloudy, as microbes grow in it
* The greater the turbidity, the larger the population size
Psychrophile
Psychotrophs
Mesophile
Thermophile
Hyperthermophile
Neutrophils
Acidophile
Alkalinophile
Halophile
Psychrophile - Cold-loving
Psychotroph - Cold-tolerant
Mesophile - Moderate-temperature-loving
Thermophile - Heat-loving
Hyperthermophile - Thrive in extreme hot
Neutrophile - Grow best in a narrow range around neutral pH
Acidophile - Grow best in acidic habitats
Alkalinophile - Live in alkaline soils and water
Halophile - Salt-loving
Microorganisms that catabolism sugars into ethanol and hydrogen gas would most likely be categorized as?
Heterolactic fermenters
True or false: in general, ATP is generated in catabolic pathways and expended in anabolic pathways
True
rRNA
Codon
tRNA
Genetic code
mRNA
- rRNA -> the type of ribonucleic acid that is part of the ribosome and protein complex that synthesizes other proteins
- Codon -> a group of three nucleotides in RNA that code for specific amino acids or for termination of the protein chain
- tRNA -> the ribonucleic acid whose function is to deliver the amino acids into position for protein synthesis
- genetic code -> the sequence of nucleotides that specifies sequences of amino acids in protein synthesis
- mRNA -> the ribonucleic acid that carried the code transcribed from DNA and directs protein synthesis
A bacterial genome is typically what
A single circular DNA molecule
