MICROPENIS Flashcards
benign
The vast majority of microbes are “benign”. Most are either directly or
indirectly beneficial to us.
*A few are pathogenic
*They decompose organic waste
*They are producers in the ecosystem (by photosynthesis)
*Help in animal digestion and vitamin production
*Commercial uses include chemicals, therapeutic drugs and more
Luis Pasteur
He started off by demonstrating the presence of microbes in the air. He used a cotton plug that caught germs to filter the air in order to do this. The microbes were then examined under a microscope, and he found that many of them matched the descriptions made by researchers who had previously investigated broths. The sterilized soup that Pasteur placed the cotton plug into became cloudy as a result of the growth of these bacteria. In particular, Pasteur demonstrated that sterile broths maintained their sterility even when exposed to air in specially designed swan-necked flasks. Airborne microorganisms gathered in the flask neck bends rather than reaching the soup. The broth could only support microbial growth when the flasks were tilted. Pasteur’s simple and elegant experiments refuted the assertions that broths or unheated air had the “vital power” necessary for spontaneous creation. They gave birth to the biogenesis theory, which states that live things are created from non-living ones.
Describe two microbial activities essential to life and three that
make our lives more comfortable.
Essential activities—(1) Conversion of nitrogen of the air into a form that is useable by plants and animals, and (2) replenishment of O2 in the atmosphere by photosynthetic microorganisms. Non-essential activities—(1) Synthesis of many products used in every day life (amino acids, vitamins, etc), (2) involvement in food and beverage production, and (3) degradation of environmental pollutants
Describing three factors that cause certain infectious diseases to become more
common.
poor sanitation, unsafe food and water, and poor hygiene
Organic molecules
*Carbohydrates
*Lipids
*Proteins
*Nucleic Acids
Chemistry of life
Carbon, hydrogen, Phosphorous, sulfur, oxygen, and nitrogen (these six elements make up 96% of our mass).
Chemical bonds
The forces that attract atoms to each other in compounds
Ionic bond
the attractive electrostatic force between a negative ion and a positive ion
covalent bond
Atoms that do not have filled valence shells may share pairs of valence electrons
Carbohydrates (monomer and Polymer)
Monosaccharide (monomer) polysaccharide (polymer)
Proteins (monomer and Polymer)
Amino acids (monomer) polypeptide (polymer)
Lipids (monomer and Polymer)
Fatty acid, glycerol (monomer) Lipid (polymer)
Nucleic acids (monomer and Polymer)
Nucleotide (monomer) Nucleic acid (polymer)
Monosaccharides
Glucose, Fructose, Galactose
Disaccharides
Maltose, Lactose, Sucrose
Polysaccharides
Starches, Fibers, Glycogen
Lipids
Phospholipids, triglycerides, sterols
Hydrogen bonds
are weak bonds formed when a hydrogen atom in a polar molecule is attracted to an electronegative atom in the same or another polar molecule.
Prokaryotes
-lack membrane
bound organelles
-lack membrane
a bound nucleus
-Archaea
-Bacteria
Eukaryotes
-have several membrane bound organelles.
-have a membrane bound nucleus
-much larger in comparison to prokaryotes in the
order of 100X
-Eukarya
Viruses
consist of DNA or RNA, surrounded by a protein coat. They are obligate intracellular parasites and collectively infect of all forms of life.
Viroids
consist of only RNA, with no protein coat. Like viruses, they are obligate intracellular agents. Viroids cause a number of plant diseases.
Prions
consist only of proteins. Prions are simply misfolded versions of normal cellular proteins found in the brain.
cytoplasmic membrane
is a thin, delicate structure that
surrounds the cytoplasm and defines the boundary of the cell.
The membrane is selectively permeable. Molecules move through the membrane by a variety of mechanisms
Simple diffusion
a passive process in which molecules move from a region of high
concentration to one of low concentration, until equilibrium is reached.
Osmosis
a passive process in which water moves across the cell membrane down its
concentration gradient from high water concentration (low solute concentration) to
low water concentration (high solute concentration).
facilitated diffusion
(a passive process in which molecules cross the
membrane via transport proteins called permeases or carriers),
active transport
(that moves molecules against their concentration gradient
and thus requires energy expenditure; energy is provided by ATP or the
proton motive force)
Diplococci
two cocci cells stuck together
Streptococci
describes multiple chains
Staphylococci
produce grape-like
clusters
Gram-positive wall
thick peptidoglycan layer and there are teichoic acids in
the wall but there is no outer membrane.
(Bacteria stain purple if positive)
The Gram-negative wall
has a thin layer of peptidoglycan and an outer membrane containing lipopolysaccharide (LPS).
Between the cytoplasmic membrane and the outer membrane is the periplasm.
(Bacteria stain pink if negative)
LPS
It has two components: lipid A and O antigen. O antigen
can be used to identify bacteria. Lipid A alerts the immune system to microbial invaders when present in low amounts. In high amounts however, LPS can cause shock and even death – it is an ENDOTOXIN.
Peptidoglycan (Murein) Structure
contains N-acetyl glucosamine and N-acetylmuramic acid and several different amino acids.
Capsules and slime layers
which are used by cells for attachment to surfaces, and
creating biofilms e.g. dental plaque, a biofilm on teeth. Some capsules also function to protect cells from phagocytosis.
Flagella
which are appendages composed of the protein flagellin, and are used for movement.
Pili
which are shorter and firmer than flagella and are composed of the protein pilin.
Pili called fimbriae are used for attachment to surfaces; sex pili are used in genetic exchange.
Chemotaxis
Movement towards or away
from a substance
*Positive chemotaxis: towards
the attractant
*Negative chemotaxis: away
from the attractant
Transport proteins
which function either as channels or carriers.
Endocytosis
(including receptor-mediated endocytosis) and pinocytosis, the
uptake of small molecules or drops of liquid.
Phagocytosis,
the engulfment of bacteria and debris by specialized cells
Exocytosis
the reverse of endocytosis by which debris is released from a cell
Electron microscopes (transmission and scanning)
can magnify up to 100,000-
fold and are used to examine fine details of cell structure. Information is also given on
scanning probe microscopes such as atomic force microscopes.
principles of light microscopy
magnification, resolution, refraction, and contrast.
Simple staining
a single dye is used. Typically the dye is basic and has a positive charge; it stains bacterial cells, which have many negatively charged components.
negative staining
Acidic dyes have a negative charge and are used for negative staining, in which the
background is colored, rather than the cells.
Differential staining
is used to distinguish between groups of bacteria. The most commonly used are the Gram stain and the acid-fast stain. The Gram stain differentiates between Gram-positive bacteria (which stain purple) and Gram-
negative bacteria (which stain pink).
Special stains
including the capsule stain, the endospore stain, the flagella stain, and fluorescent stains that are used in a technique called immunofluorescence.
Binary fission
Bacteria and archaea multiply by binary fission
Exponential
Cell growth is exponential
generation time
he time it takes for a generation to double is the generation time
biofilms
In nature, most microbes grow in polymer-encased communities called biofilms
- Biofilms
may be either damaging (for example, those involved in infections) or beneficial (for
example, they are used in bioremediation). The majority of bacterial infections involve
biofilms. Treatment of these infections is difficult because microbes within the biofilm often
resist the effects of antibiotics as well as the body’s defenses.
In the laboratory, prokaryotes are generally grown in ______
pure cultures
Pure cultures are typically obtained using the _________in which individual
_______ are isolated using __________
streak-plate method; colonies; aseptic technique
Once a pure culture has been obtained, it can
be maintained as a _________
stock culture
open system
nutrients are continually added and wastes are removed, so that cells are maintained in a state of constant growth.
closed system
nutrients are not renewed and wastes are not renewed. The cells follow distinct stages of growth, called a growth curve.
lag phase
cells are metabolically active but do not divide.
exponential or log growth phase
cells divide and their numbers increase logarithmically. Cells are most sensitive to antibiotics during this time. They also produce primary and secondary metabolites during this phase, which may be commercially valuable.
stationary phase
When the nutrient level in the system is too low to sustain growth, cells enter the stationary phase, and the total number of cells in the population remains fairly
constant.
death phase
the number of cells in the population declines as cells die at
a constant rate.
period of prolonged decline
during which most cells die, but a few are able to survive.
Psychrophiles
optimum between –5°C and 15°C.
Psychrotrophs
optimum between 15°C and 30°C but grow at lower
temperatures as well. Refrigeration slows growth but does not kill these
microbes.
Mesophiles
optimum between 25°C and about 45°C. Pathogens, adapted to
growth in the human body, typically have an optimum between 35°C and 40°C
although some may prefer lower temperatures and grow in cooler regions of
the body e.g. M. leprae, the causative organism of leprosy.
Thermophiles
optimum between 45°C and 70°C
Hyperthermophiles
optimum of 70°C or greater.
Obligate aerobes
have an absolute requirement for oxygen (O2). They use it
in aerobic respiration, an energy-harvesting process.
Facultative anaerobes
grow better if O2 is present, but can also grow without
it.
Obligate anaerobes
cannot multiply if O2 is present
Microaerophiles
require low amounts of O2 (2% to 10%).
Aerotolerant anaerobes
indifferent to O2. They can grow in its presence,
but do not use it to harvest energy. They are also called obligate fermenters,
because fermentation is their only metabolic option.
neutrophiles
Most microbes are neutrophiles—they live and multiply within the range of
pH 5 (acidic) to pH 8 (basic), and have a pH optimum near neutral (pH 7).
Acidophiles
grow optimally at a pH below 5.5.
Alkaliphiles
grow optimally at a pH above 8.5.
Water availability
All microorganisms require water for growth. If the solute
concentration is higher in the medium than in the cell, water diffuses out of the cell due to osmosis. This causes the cytoplasm to dehydrate and shrink from the cell wall,
a phenomenon called plasmolysis
Microbes that tolerate high salt concentrations, up to approximately 10% NaCl, are _________
halotolerant
halophiles
require high levels of sodium chloride.
heterotrophs
use organic carbon; medically important bacteria are typically heterotrophs.
autotrophs
use inorganic carbon in the form of carbon dioxide (CO2). They play a critical role in the cycling of carbon in the environment
Phototrophs
harvest energy from sunlight
chemotrophs
extract energy from chemicals.
Photoautotrophs
use the energy of sunlight to make organic compounds from CO2 in the atmosphere
Photoheterotrophs
use the energy of sunlight and obtain their carbon from organic
compounds.
Chemolithoautotrophs
use inorganic compounds for energy and obtain their carbon
from CO2.
Chemoorganoheterotrophs
use organic compounds for both energy and carbon.
complex medium
contains a variety of ingredients such as meat juices and
digested proteins, and is used for routine purposes. Examples include blood agar, and chocolate agar.
chemically defined medium
is composed of specific amounts of pure chemicals,
so its exact chemical composition is known. This type of medium is generally used
only for certain research experiments e.g. glucose-salts agar.
Selective media
contain an ingredient that inhibits the growth of certain species in a mixed sample, while allowing the growth of the species of interest e.g. MacConkey
agar, which inhibits the growth of Gram-positive cells.
Differential media
contain a substance that certain microbes change in a
recognizable way e.g. blood agar (showing hemolysis) and MacConkey agar (differentiating between lactose-fermenting bacteria [pink-red] and lactose-negative bacteria [colorless]).
Direct cell counts
are used to determine total number of cells including living and
dead cells; examples are direct microscopic counting and cell-counting instruments such as the Coulter counter or the flow cytometer.
Viable cell counts
are used to determine the number of microorganisms capable of
growing in a given set of conditions; includes plate counts, membrane filtration and most probable number.
Biomass
can be correlated to cell number. Biomass can be measured by measuring turbidity or total microbial weight.
Taxonomy order
Kingdom, Phylum, Class, Order, Family, Genus, Species
NT=N0X2^N
NT = NUMBER OF CELLS IN POPULATION
N0 = ORIGINAL NUMBER OF CELLS IN THE POPULATION
N - NUMBER OF DIVISIONS
Catabolism
is the set of chemical reactions that degrade compounds, releasing their energy. Cells capture that energy and use it to make ATP—the energy currency of the cell.
Anabolism
is the set of chemical reactions that cells use to synthesize and assemble the subunits of macromolecules, using ATP for energy.
metabolic pathway
The series of chemical reactions that
converts a starting compound to an end product
Enzymes
drive chemical reactions; these are molecules (usually
a protein) that function as biological catalysts, speeding up the conversion of one substance, the substrate, into another, the product, by lowering the activation energy—the energy it
takes to start a reaction
co-factor
Some enzymes require the assistance of an
attached non-protein component called
denature
losing their characteristic 3D shape.
Glycolysis
converts glucose to pyruvate and generates 2 ATP (net) by substrate-level phosphorylation, 2 NADH + 2 H+, and six different precursor metabolites
pentose phosphate cycle
is an alternative break down glucose, and generates
various amounts of NADPH + H+, and two different precursor metabolites
transition step
links glycolysis or the pentose phosphate pathway to the TCA
cycle; it is repeated twice to oxidize two molecules of pyruvate to acetyl-CoA, and generates 2 NADH + 2 H+ and one precursor metabolite
TCA cycle
is repeated twice to incorporate two acetyl groups and generates 2 ATP by substrate-level phosphorylation, 6 NADH + 6 H+, 2 FADH2 and two different precursor metabolites
Hydrogen bacteria
oxidize hydrogen gas.
Sulfur bacteria
oxidize hydrogen sulfide.
Iron bacteria
oxidize reduced forms of iron.
Nitrifying bacteria
include two groups of bacteria; one oxidizes ammonia (forming
nitrite), and the other oxidizes nitrite (producing nitrate).
photosynthesis
conversion of radiant energy into chemical energy
carbon fixation
Chemolithoautotrophs and photoautotrophs incorporate carbon dioxide (CO2) into organic compounds
Calvin cycle
(1) Incorporation of CO2 into an organic compound; (2)
reduction of the resulting molecule; and (3) regeneration of the starting compound.
genome
The genetic material of a cell
cell division
(1) replicate its DNA and (2), express its genes, which involves copying the information of DNA into RNA
(transcription) and then decoding the RNA to synthesize a protein (translation).
DNA
is a double-stranded, helical structure composed of nucleotides. Each nucleotide contains a 5-carbon sugar (deoxyribose), a phosphate group, and one of four different
nucleobases (A, T, G, or C). The two strands in the DNA helix are complementary and are held together by characteristic bonding of A to T and G to C, called base pairing
transcription
It involves copying a gene’s DNA sequence to make an RNA molecule.
Translation
decoding of the information in mRNA to create the specified protein.
Antigenic variation
random changing in the characteristics of certain surface proteins.
Phase variation
is the random switching on and off of
certain genes. This can help a microbe colonize different habitats.
constitutive
(synthesized continuously)
inducible
(synthesized when needed)
repressible
(routinely produced but synthesis
can be turned off when they are not needed).
repressor
blocks transcription when it binds
to an operator
activator
enhances transcription when it binds to an activator-binding site
Inducers
bring about gene expression by binding either to repressors (disabling them)
or to activators (allowing them to attach to the activator-binding site).
lac operon
model for gene regulation
Carbon catabolite repression (CCR)
prevents transcription of the lac operon
when glucose is available
inducer exclusion.
A type of CCR that prevents a carbon/energy source from being transported into the cell
Mutation
changes the existing nucleotide sequence of a cell’s DNA, which is then passed on to the progeny through vertical gene transfer
Horizontal gene transfer
is the movement of
DNA from one organism to another. Like mutations, the changes are then passed on to the
progeny by vertical transfer.
auxotroph
mutant that requires a growth factor
prototroph
A wild type organism that does not require additional growth factors
base substitution
-most common mutation
-occurs during DNA synthesis when an incorrect nucleotide is incorporated.
silent mutation,
the change generates a codon that translates into the same
amino acid as the original.
missense mutation
results when the altered codon codes for a different amino
acid.
nonsense mutation
occurs when the base substitution creates a stop codon,
resulting in a shorter (truncated) and often non-functional protein.
Transposons
jumping genes, are pieces of DNA that can move from one location to another in a cell’s genome, a process called transposition.
insertional inactivation.
The gene into which a transposon
jumps is inactivated by the event
stop codons
UAG, UAA, UGA
