1 Flashcards
cell theory
All life is made of cells, cells come from other cells, cells are the fundamental unit of life
six basic categories of microorganisms
bacteria, archaea, algae, fungi, protozoans, helminths
acellular microorganisms
viruses, prions
domains of life
Bacteria, Archaea, Eukarya
all cells possess these:
cytoplasm, plasma membrane, one or more chromosomes made from DNA, and ribosomes
prokaryotes vs eukaryotes
prokaryotes lack a nucleus, do not have membrane bound organelles, have DNA in the for, of single, circular chromosome. eukaryotes have a nucleus, have membrane bound organelles, have 1+ chromosomes in linear strand, tend to be bigger than prokaryotes
cell morphology
cell shape
Bacteria: unicellular or multicellular?
unicellular
prokaryotic microorganisms
bacteria, archaea
bacterial cell wall contains
peptidoglycan
bacterial replication/reproduction
binary fission, asexual
bacteria: pathogenic or not?
can be pathogenic, not all are pathogens
archaea: unicellular or mutlicellular?
unicellular
archaea replication/reproduction
binary fission, asexual
archaea: pathogenic or not?
not human pathogens
archaea differs from bacteria in
evolutionary history, genetics, metabolic pathways, and cell wall/membrane compostition
archaea cell wall composed of
pseudopeptidoglycan
eukaryotic microorganisms
algae, fungi, protozoa, helminths
algae: unicellular or multicellular?
can either be unicellular or mulitcelluar
algae: pathogenic or not?
not known to be human pathogens
algae cell wall composition
cellulose
algae replication/reproduction
mitosis, both sexually and asexually
protozoa: unicellular or multicellular?
unicellular
protozoans: pathogenic or not?
most are harmless, some are human pathogens
fungi: unicellular or mulitcellular?
can be unicellular (yeasts) and multicellular (mold)
fungi cell wall composition
chitin
fungi: pathogenic or not?
can cause disease in humans
helminths: unicellular or multicelluar?
multicellular
what are helminths?
parasitic worms that aren’t technically microorganisms, their eggs are
helminths: pathogenic or not?
can be human pathogens
what are viruses
proteins and genetic material (either DNA or RNA) that are inert outside of host
viruses: pathogenic or not?
can be human pathogens
what are prions
misfolded proteins
what is the cause of the formation of a prion?
genetic mutation, can also happen spontaneously
Prions: pathogens or not?
can be pathogenic (causes transmissible spongiform encephalopathy)
taxonomy definition
classification, description, and naming of living organisms
classification definition
practice of organizing organisms into different groups based on their characteristics
phylogeny definition
takes into account of the evolutionary relationships of all different species of organisms
binomial nomenclature
two word naming system for identifying microorganisms by genus and species
Bergey’s Manuals
standard reference for identifying and classifying different prokaryotes
Theory of spontaneous generation
theory that life arises from nonliving material
endosymbiotic theory
theory that eukaryotic organelles, mitochondria and chloroplasts, came from prokaryotic origin
Germ theory of disease
states that microorganisms known as “germs” can lead to disease
last universal common ancestor
all life can be traced back to one ancestor
epidemology
concerns the geographical distribution and timing of infectious disease and how they are transmitted
goal of epidemology
recognizing and controlling outbreaks
etiology
included in epidemology, the study of the causes of disease and investigation of disease transmission
sporadic disease
seen only occasionally and w/o geographic concentration
endemic diseases
diseases that are constantly present at a low level in a population within a certain geographical area
epidemic
diseases for which a larger than expected number of cases occur in a short amount of time within a certain geographical area
pandemic
epidemics that occur on a worldwide scale
Koch’s Postulates purpose
determines whether a particular organism is the cause of a particular disease
First Koch’s postulate
the suspected pathogen must be found in every case of the disease and not in healthy individuals
Second Koch’s Postulate
the suspected pathogen can be isolated and grown in pure culture
Third Koch’s Postulate
A healthy test subject infection w/ the suspected pathogen should present the same signs and symptoms of the disease as in postulate 1
Fourth Koch’s Postulate
the pathogen must be reisolated from the new host and must be identical to postulate 2
Molecular Koch’s Postulates purpose
to identify a specific gene that may cause an organism to be pathogenic
First Molecular Koch’s Postulate
The phenotype (signs and symptoms of disease) should be associated w/ only the pathogenic strain of a species
Second Molecular Koch’s Postulate
Inactivation of suspected gene(s) associated w/ pathogenicity should result in measurable loss of pathogenicity
Third Molecular Koch’s Postulate
Reversion of the inactive gene should restore the disease phenotype
pathogenicity definition
the ability of a microbial agent to cause disease
virulence definition
degree to which an organism is pathogenic
Median infectious dose
number of pathogen cells required to cause active infection in 50% of subjects
median lethal dose
number of pathogenic cells required to kill 50% of infected subjects
Emerging infectious disease
either new to human population or has shown an increase in prevalence in the previous 20 years
Reemerging infectious disease
increasing in frequency after a previous period of decline
reservoirs
where pathogens normally reside to persist over long period of time
carrier
an individual capable of transmitting a pathogen w/o displaying symptoms
passive carrier
contaminated w/ pathogen and can mechanically transmit it to another host; however passive carriers are not infected
active carrier
infected individual who can transmit disease to others
asymptomatic carriers
active carriers who do not present signs and symptoms of disease despite being infected
living reservoirs
animals can act as reservoirs of human disease and transmit the infectious agent to humans through direct or indirect contact
definitive hosts
host in which the parasite reaches sexual maturity
intermediate hosts
host in which parasite go through several immature life cycles or reproduce asexually
first step in transmission
transmission from reservoir to individual
second step in transmission
individual transmits infectious agent to other susceptible individuals
third step in transmission
pathogenic microorganisms employ diverse transmission mechanisms
contact transmission
direct transmission (person to person) and indirect transmission (inanimate objects contaminated by pathogens)
vehicle transmission
transmission of pathogens through food, water, or air
vector transmission
transmitted by a mechanical or biological vector
Mechanical vector
an animal that carries a pathogen from one host to another w/o being infected itself
Biological vector
pathogen reproduces within a biological vector that transmits the pathogen from one host to another (bug bites)
nosocomial infections
infections spread in a healthcare setting
light microscopes
brightfield microscopes, darkfield microscopes, phase-contrast, differential interference contrast, fluoroscence, confocal scanning laser, and two-photon
simple staining
single dye is used to emphasize particular structure of a specimen, will make all organisms the same color
differential staining
distinguishes organisms based on their interactions w/ multiple stains
First step in Gram Staining
crystal violet is applied to a heat fixed smear, making all cells purple
Second step in gram staining
a mordant, iodine, is applied to set the crystal violet and make it stay contained in thick layers of peptidoglycan
Third step in gram staining
Decolorizing agent, alcohol is added, removes crystal violet from thin layers of peptidoglycan, making them colorless
Fourth step in gram staining
A counterstain, safranin, is added and color the decolorized thin layers of peptidoglycan pink
Acid fast stain purpose
differentiates between two types of gram+ cells: those that have waxy mycolic acid in their cell wall, and those that don’t
First step in acid fast staining
waxy, acid fast cells will retain the carbolfuchsin after a decolorizing agent is added (acid-alcohol solution)
Second step in acid fast staining
a secondary counterstain, methylene blue, is then applied which renders non acid fast cells blue
Capsule staining technique
negative staining technique used, capsules cannot pick up dye, appear as halo around cell
common negative stains for capsule staining
india ink or nigrosin
endospore staining first step
Schaeffer-Fulton method uses heat to push primary stain (malachite green) into the endospore
endospore staining second step
wash with water to decolorize the cell, endospore remain green
endospore staining third step
cell is counterstained pink w/ safranin
Important genera of endospore producing bacteria
Bacillus and Clostridium
Flagella staining
thickens flagella w/ mordant (tamic acid or potassium alum) which coats the flagella; specimen is stained w/ pararosaniline or basic fuchsin
Cell wall function
envelops cell membrane, protecting the cell from changes in osmotic pressure
isotonic medium
solute concentration equal in and out of cell; water moves equally in and out of cell
hypertonic medium
solute concentration greater outside the cell, water diffuses out of cell
hypotonic solution
solute concentration greater inside the cell, water diffuses into cell
plasmoslysis
cell membrane shrinks and detaches from cell wall in a hypertonic solution
tugor pressure
pressure of cell membrane’s expansion on the cell wall when a cell is in a hypotonic environment
Nucleoid-associated proteins
assist in the packing and organization of the chromosome in prokaryotic organisms
Plasmids
small, circular, double-stranded DNA molecules found in some prokaryotic cells that are not part of the chromosome
Prokaryotic ribosomes
made from proteins and RNA, found in cytoplasm, called 70S ribosomes
Inclusions
some prokaryotic cells have ability to store excess nutrients within cytoplasmic structures called inclusions
endospores
structures that protect the cell in a dormant state when environmental conditions are unfavorable
Sporulation
the process by which vegetative cells transform into endospores:
dna replicates, septum forms around DNA, divides cell asymmetrically, …, endospore is released upon disintegration of mother cell
germination
process of a cell becoming vegetative again after being an endospore; cell becomes metabolically active again and is able to perform all its normal functions
Fluid mosaic model
refers to the ability of the cell membrane components to move fluidly within the plane of the membrane, as well as the mosaic like composition of the components (lipids and proteins)
plasma membrane structure
bilayer composed of phospholipids formed w/ ester linkages and proteins (for bacteria and eukaryotes) can be monolayer for some archaea
passive transport (simple diffusion)
molecules moving from higher concentration to lower concentration across membrane
facilitated diffusion
a type of passive transport in which larger molecules that need carriers (protein channels in the membrane) that ferry them across the membrane
active transport
cell moves molecules across their membrane against the concentration gradient, require ATP
Group translocation
molecule moves into cell against gradient and is chemically modified so that it does not require transport against an unfavorable concentration gradient
photosynthetic membrane structures
infolding of the plasma membrane that encloses photosynthetic pigments such as green chlorophylls and bacteriochlorophylls
composition of peptidoglycan
long chains of alternating molecules of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)
gram positive bacteria cell wall
cell wall consisting of many layers of peptidoglycan and are commonly embedded with teichoic acid, carbohydrate chains that extend through and beyond the peptidoglycan layer
Gram negative bacteria cell wall
thin layer of peptidoglycan, periplasmic space, outermembrane w/ lipoproteins and porein proteins embedded. outer leaflet of outermembrane contains lipopolysaccharide (LPS), which functions as an endotoxin
glycoalyces
structures exterior to the cell wall, a sugar coat, two important types: capsules and slime layers
capsules
organized layer outside of the cell wall and usually composed of polysacchs or proteins
slime layers
loosely attached to cell wall, composed of polysacchs, glycoproteins, or glycolipids
function of glycoalyces
allow cell to adhere to surfaces aiding in the formation of biofilms. protects them from desiccation, predation, and hinders the action of antibiotics and disinfectants
filamentous appendages functions
attach to other surfaces, transfer DNA, or provide movement
filamentous appendages types
fimbriae, pili, and flagella
fimbriae
short, bristle like proteins that extend out of the cell surface by the hundreds
fimbriae functions
enable a cell to attach to surfaces and other cells; pathogenic bacteria adherence to host cells is important for colonization, infectivity, and virulence
pili
longer, less numerous protein appendages that aid in the attachment to surfaces and transfer of DNA
flagella
stiff, spiral filaments that are composed of flagellin protein subunits and act as motors
polar flagella
flagella located at one or both ends of a bacterium
peritrichous flagella
flagella that cover the entire surface of a bacterial cell
polar arrangements of flagella
monotrichous (one flagella), amphitrichous (two flagella on opposite ends), and lophotrichous (many flagella on one end)
flagella movement
increasing the length of runs and decreasing lengths of tumbles
phototaxis
bacteria move in response to light
magnetotaxis
bacteria move in response to magnetic fields
chemotaxis
bacteria move in response to chemical gradients
axial filaments
endoflagella that are located in periplasmic space and wraps around the cell giving it a corkscrew shape (spirochetes, spirilla), aids in movement
Mycobacterium
genera of acid-fast bacilli that are covered in a waxy coat of mycolic acid
classes of Gram positive bacteria
Actinobacteria and Bacilli
Class Actinobacteria
comprises high G+C gram positive bacteria, which have more than 50% guanine and cytosine nucleotides in their DNA
Class Bacilli
comprises low G+C gram+ bacteria, which have less than 50% guanine and cytosine nucleotides in their DNA.
Mycoplasmas
genera of bacteria that do not posses a cell wall
chemotherapy
broad term that refers to any use of chemicals or drugs to treat disease
antimicrobial drugs
typically destroy or interfere w/ microbial structures or enzymes either killing microbial cells or inhibiting their growth
factors important when choosing an antimicrobial drug
bacteriostatic vs bactericidal mechanisms, spectrum of activity, dosage and route of administration, potential side effects, and potential interactions between drugs
bacteriostatic drugs
cause reversible inhibition of growth, with bacterial growth restarting after elimination of drug
bactericidal drug
kill their target bacteria
spectrum of activity
relates to the diversity of targeted bacteria: narrow spectrum or broad spectrum
narrow-spectrum drug
only targets specific subsets of bacterial pathogens (ex: targeting only gram positive cells)
broad-spectrum drug
targets a wide variety of bacterial pathogens, can harm normal microbiota
superinfection
a secondary infection in a patient having a preexisting infection (broad-spectrum antibiotic can cause this)
dosage
amount of medication given during a certain interval of time
factors to consider when selecting dosage
patient’s mass, consideration for how drugs are metabolized and eliminated, half-life of drug
half-life
rate at which 50% of the drug is eliminated from plasma (time in between doses), longer half-life=more serious side effects
route of administration
method used to introduce drug to body
drug interactions
a drug’s inaction w/ another drug: synergistic or antagonistic
synergistic interactions
two antibacterial drugs administered together that are better than either drug alone
antagonistic interactions
effects depend on drugs involved by may cause: loss of drug activity, decreased therapeutic levels due to increased metabolism and elimination, or increased potential toxicity due to decreased metabolism and elimination
selective toxicity
selectively killing or inhibiting growth of a microbial target while causing minimal damage to no harm to the host
modes of action (for antibacterial drugs)
the way in which a drug affects microbes at a cellular level: inhibitors of cell wall synthesis, inhibit biosynthesis of proteins, disrupt membranes, inhibit nucleic acid synthesis, inhibit metabolic processes, inhibit ATP production
Therapeutic Index
difference between the dose given to the patient and the dose that would cause side effects in the patient
inhibitors of cell wall synthesis
several different classes of antibacterials block steps in the biosynthesis of peptidoglycan, making cells more susceptible to osmotic lysis and are bactericidal in action
Beta-Lactam Drugs function (inhibitors of cell wall synthesis)
block the crosslinking of peptide chains during the biosynthesis of new peptidoglycan in the bacterial cell wall
Beta-Lactam drug types
penicillin, cephalosporins, monobactam (aztreonam), carbapenems
Penicillins
penicillin G and V are natural antibiotics from fungi. semisynthetic penicillins include: ampicillin, amoxicillin, and methicillin
Cephalosporins
cephalosporin C is a natural antibiotic derived from fungi. semisynthetic cephalosporins include: first, second, third, fourth, and fifth generation cephalosporins
monobactam
only drug used is aztreonam, narrow-spectrum against gram- bacteria and is semisynthetic
Carbapenams
semisynthetic, broad-spectrum active against gram+ and gram- pathogens
glycopeptide function (inhibitor of cell wall synthesis)
binds to end of peptide chain of cell wall precursors, creating a structural blockage that prevents cell wall subunits from being incorporated into peptidoglycan structure.
vancomycin
member of class glycopeptide. natural antibiotic that is bactericidal towards gram+ bacteria
Bacitracin (cell wall synthesis inhibitor)
drug that blocks the activity of a specific cell-membrane molecule that is responsible for the movement of peptidoglycan precursors, preventing their incorporation into the cell wall. broad-spectrum against gram+ and gram-
aminoglycosides function (protein synthesis inhibitor)
bind to the 30S subunit of bacterial ribosomes, impairing the proofreading ability of the ribosomal complex which creates faulty proteins that kill the bacterial cells
aminoglycoside types
streptomycin, gentamycin, neomycin, and kanamycin are broad spectrum bactericidal drugs
tetracyclines function (inhibitor of protein synthesis)
blocks the association of tRNA w/ the ribosome during translocation
tetracycline types
a natural antibacterial but semisynthetic versions include: doxycycline and tigecycline, which are bacteriostatic broad-spectrum antibacterials
Protein synthesis inhibitors that bind to the 50S subunit function
block elongation of proteins by inhibiting peptide bond formation between specific combinations of amino acids
Classes of 50S protein synthesis inhibitors
macrolides, lincosamides, oxazolidinones
Macrolides types (50S protein inhibitors)
natural erythromycin, semisynthetic azithromycin and telithromycin are broad-spectrum bacteriostatic
lincosamides types (50S protein synthesis inhibitors)
natural lincomycin and semisynthetic clindamycin which are narrow spectrum bacteriostatic
chloramphenicol (50S inhibitor)
not a drug class, bacteriostatic and broad-spectrum. causes anemia by targeting mitochondrial ribosomes within hemopoietic stem cells
oxazolidinone function (50S inhibitor)
interferes w/ the formation of the initiation complex for translocation and then prevents translocation of the growing protein from ribosomal A site to P site
oxazolidinone types (50S inhibitor)
include drug linezolid, a broad-spectrum bacteriostatic
Classes of membrane function inhibitors
polymyxins, lipopeptides
Polymyxin function (membrane function inhibitor)
interact w/ LPS in the outer membrane of gram- bacteria, killing the cell through the eventual disruption of the outer and cytoplasmic membrane
Polymyxin types
polymyxin B and E (colistin) are natural, narrow-spectrum against gram- bacteria, bactericidal
Lipopeptide function (membrane function inhibitor)
insert into the cytoplasmic membrane of gram+ bacteria, disrupting the cell membrane and killing the cell
Lipopeptide types
daptomycin is a natural, narrow-spectrum against gram+ bacteria, bactericidal
Classes of Inhibitors of nucleic acid synthesis
rifamycin and fluoroquinolones
Rifamycin function (inhibitor of nucleic acid synthesis)
inhibit bacterial RNA polymerase activity, blocks transcription, killing the cell
Rifamycin types
rifamycin is semisynthetic narrow-spectrum w/ activity against gram+ and limited gram-, bactericidal. active against M. tuberculosis.
Fluoroquinolone function (nucleic acid synthesis inhibitor)
inhibit activity of DNA gyrase and block DNA replication, killing the cell
Fluoroquinolone types
ciprofloxacin, ofloxacin, moxifloxacin, levofloxacin are semisynthetic, broad-spectrum, bactericidal drugs
Sulfonamides and sulfones function (inhibitors of metabolic pathways)
target folic acid synthesis by inhibiting the enzyme involved in the production of dihydrofolic acid, are structural analogs of PABA
Sulfonamides and sulfone types
sulfamethoxazole (sulfonamide) and dapsone (sulfone) are synthetic, bacteriostatic, broad spectrum drugs
Trimethoprim (inhibitor of metabolic pathways)
targets folic acid synthesis by inhibiting the enzyme involved in the production of tetrahydrofolic acid, structural analog of dihydrofolic acid. synthetic, bacteriostatic, broad-spectrum
Isoniazid (inhibitor of metabolic pathways)
prevents mycolic acid synthesis, which is essential for mycobacterial cell walls. narrow-spectrum against Mycobacterium spp.
Inhibitor of ATP synthase
synthetic class called the diaryquinolones use novel mode of action that specifically inhibits mycobacterial growth
Diarylquinolone function (inhibitor of ATP synthase)
bedaquiline appears to interfere w/ the function of ATP synthases, perhaps by interfering w/ the use of hydrogen ion gradient, leading to reduced ATP production
Antifungal drugs’ mode of action
most common mode of action is the disruption of cell membrane, take advantage of the small differences between human and fungi in the biochemical pathways that synthesize sterols.
factors that accelerate the evolution of drug resistance
overuse and misuse of antimicrobial, inappropriate use of antimicrobials, subtherapeutic dosing, and patient non compliance w/ the recommended course of treatment
mechanisms for drug resistance
enzymatic modification of drug, modification of antimicrobial target, prevention of drug penetration, prevention of drug accumulation
drug modification or inactivation
resistant genes may code for enzymes that modify an antimicrobial, inactivating it or destroying it through hydrolysis
drugs that drug modification or inactivation targets
aminoglycosides, beta-lactams, rifampin, macrolides, and lincosamides
prevention of cellular uptake
inhibiting accumulation of drug, which prevents it from getting to its target. Can involve changes in the outer membrane lipid composition, porin channel selectivity, and/or porin channel concentrations
efflux pump
prevent accumulation of drug by actively transporting them out of the cell. a single efflux pump can pump multiple types of antimicrobials
drugs effected by efflux pumps
beta-lactams, tetracycline, and fluoroquinolones
target modification
many antimicrobial drugs have specific targets, structural modifications to those targets can prevent drug binding rendering the drug ineffective
target overpopulation
microbe may overproduce the target enzyme so that they are enough to carry out proper enzymatic action
enzymatic bypass
bacterial cell may develop a bypass that circumvents the need of the functional target enzyme
target mimicry
involves the production of proteins that bind and sequester drugs, preventing the drugs from binding to their target
multidrug-resistant microbes
known as “superbugs” and carry one or more resistance mechanisms making them resistant to multiple antimicrobials
cross-resistance
a single mechanism that confers resistance to multiple antimicrobial drugs (efflux pump)
ESKAPE pathogens
important superbugs: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.
MRSA
methicillin-resistant Staphylococcus aureus. opportunistic pathogens that can be spread at hospitals
VRE, VRSA, VISA
vancomycin-resistant enterococci, vancomycin-resistant S.aureus, and vancomycin-intermediate S. aureus resist by target modification involving structural changes to the peptide component of peptidoglycan, preventing vancomycin from binding
antimicrobial susceptibility testing
testing the effectiveness of antimicrobial drugs in a clinical lab
Kirby-Bauer Disk Diffusion test
only provides info on the antibacterials to a bacterial pathogen is susceptible or resistant. measured by zone of inhibition
Dilution tests
used to determine a particular drug’s minimal inhibitory concentration (MIC) and the minimal bactericidal concentration
minimal inhibitory concentration
lowest concentration of a drug that inhibits the visible growth of bacteria
Minimal bactericidal concentration
lowest concentration of a drug that kills greater than or equal to 99.9% of bacteria
macronutrients
make up 99% of dry weight of cells and include hydrogen, carbon, oxygen, nitrogen, phosphorus, and sulfur
complex (undefined) media
contain all of CHONPS in an organic form plus growth factors that allow fastidious bacteria to grow. exact chemical composition of components is unknown
substances that make a media undefined
extract/digests of plants, animals, yeasts. Peptone, yeast extract, BHI, animal tissue, pancreatic digest casein
micronutrients (trace elements)
required by some cells in very small amount and include sodium, potassium, magnesium, zinc, iron, calcium, molybdenum, copper, cobalt, manganese, or vanadium
isomers
molecules w/ same atomic makeup but different structural arrangements
structural isomers
compounds that have identical molecular formula but different bonding sequences
stereoisomers
isomers that differ in spatial arrangement of atoms
Macromolecules
carbohydrates, proteins, lipids, nucleic acids
functions of carbohydrates
energy, storage, structure
functions of lipids
energy storage, membrane structure
functions of nucleic acids
storage, transfer of genetic material, protein synthesis instructions
function of proteins
enzymes, receptors, transport, structure
monosaccharides
simplest carbohydrate. building blocks, monomers, for the synthesis of polymers
disaccharides
two monosaccharides linked together by a covalent glycosidic bond
polysaccharides
polymer composed of hundreds of monosaccharides. cellulose makes up cell walls in plants, glycogen stores energy in animals and bacteria, starch stores energy in plants
fatty acid
lipid monomer. saturated and unsaturated fatty acids
triglyceride
lipid monomer. 3 fatty acids chemically linked to a glycerol molecule
phospholipids
complex lipids that contain a phosphate group in addition to 2 fatty acids and glycerol
isoprenoids
branched lipids that are formed by chemical modifications of the isoprene molecule. found in hydrophobic oils and waxes
sterols
steroids, another type of lipid. found in cell membrane (cholesterol in animals, ergosterol in fungi, similar compound in bacteria called hopanoid)
peptides
50 or fewer amino acids linked together
polypeptides
synthesized from up to 50 amino acids. multiple are used as subunits to build proteins
primary structure
sequence of amino acids that make up the peptide chain
Secondary structure
H bonding between amine and carbonyl groups, resulting in localized folding
Tertiary structure
large scale, 3-D shape of a single polypeptide chain. formed by interaction between R groups of amino acids
Interactions (tertiary protein structure)
disulfide bridges, H bonds, ionic bonds, hydrophobic interactions
Quaternary Structure
assemblies of several separate polypeptides, proteins are subunits
Conjugated proteins
proteins w/ a nonprotein portion, are important components of membranes
denaturation
unfolded proteins, implies loss of secondary, tertiary, and/or quaternary structure w/o loss of primary structure
defined media
complete chemical composition of the media is known
types of defined media
agar, agar+salts (AS), agar+salts+glucose (ASG)
selective media
inhibit growth of unwanted microorganisms and support growth of the organism of interest by supplying nutrient and reducing competition
types of selective media
phenylethyl alcohol agar (PEA) and MacConkey agar (MAC)
Differential media
makes it easy to distinguish between colonies of different bacteria by a change in color of the colonies or the color of the medium
types of differential media
MacConkey agar (MAC)
prokaryotic reproduction
always asexual, although horizontal gene transfer can take place
bacterial chromosome
most have single circular chromosome, some exceptions exist (B. burgdorferi has a linear chromosome)
binary fission
most common method of replication in bacteria. creates two identical daughter cells
generation time
in eukaryotes, time between the same points in the life cycle between two successive generations
doubling time
generation time but for prokaryotes. time it takes for the population to double through one round of binary fission
growth curve
microorganisms grown in a closed culture follow the same reproductive growth pattern of a lag phase, log phase, stationary phase, and death phase
lag phase
cells are gearing up for the next phase of growth. number of cells does not change, cells are growing larger and are metabolically active
log phase
cells are actively dividing by binary fission and their numbers are increasing exponentially
stationary phase
total number of living cells reaches plateau, number of new cells is equal to number of cells dying. cells switch to survival mode of metabolism, those can can undergo sporulation
death phase
medium’s nutrient are depleted, cells die in greater numbers than they are being produced
fragmentation
alternate pattern of cell division. many nucleoids that accumulate in an enlarged round cell or along a filament, leading to the generation of many new cells at once
budding
forms a long extension at one pole, the tip of the extension swells and forms a smaller cell, the bud eventually detaches from the parent cell
oxygen revolution
cyanobacteria starting releasing oxygen as byproduct, which lead to more oxygen in the atmosphere, killing all organisms that could not survive against reactive oxygen species
reactive oxygen species
highly unstable ions that can damage any macromolecule or structure they come in contact with. singlet oxygen, superoxide, peroxides, hydroxyl radical, and hypochlorite ion
obligate aerobes
cannot grow w/o abundant supply of oxygen
obligate anaerobes
killed by presence of atmospheric oxygen
facultative anaerobes
thrive in presence of oxygen but also grow w/o it using fermentation or anaerobic respiration
aerotolerant anaerobes
do not use oxygen in their fermentative metabolism but aren’t harmed by it
microaerophiles
require minimum, specific level of oxygen for growth
obligate aerobes environment
found in presence of oxygen, on human skin
obligate anaerobe environment
places devoid of oxygen such as deep sediments of soil, still waters, bottom of the deep ocean, intestinal tracts of animals
facultative anaerobe environment
found in upper respiratory tract of humans
aerotolerant bacteria environment
found in human mouth
microaerophile environment
found in gastrointestinal tract of humans
optimum oxygen concentration
the ideal oxygen concentration for a microorganism
minimum oxygen concentration
lowest concentration of oxygen that allows growth
maximum oxygen concentration
highest tolerated concentration of oxygen
enzymes that break down reactive oxygen species
superoxide dismutase, peroxidase, and catalase
peroxidases
oxidize peroxides to water
superoxide dismutase
breaks down superoxide anions
catalase
converts hydrogen peroxide to H2O and O2
neutrophiles
organisms that grow optimally within 1-2 pH from neutral. most bacteria are neutrophiles
fungi pH
thrive at slightly acidic pH of 5-6
acidophiles
microorganisms that grow optimally at a pH of less than 5.5
alkaliphiles
organisms that grow best at pH of 8-10.5
mesophiles
adapted to moderate temperatures of 20-45 degrees C
psychrotrophs
prefer colder environments of 4-25 degrees C
psychrophiles
grow at below 0 to 20 degrees C
thermophiles
grow at optimum temps of 50 to 80 degrees C
hyperthermophiles
grow at 80-110 degrees C
halophiles
require high salt concentrations for growth (3.5%)
extreme halophiles
grow in hypersaline environments such as the great salt lake and the dead sea
halotolerant
do not need high salt concentrations to grow, but will survive and divide in presence of high salt
glycolysis
means the breaking of glucose, used to generate ATP and as the first step in cellular respiration and fermentation
glycolysis process
energy investment of 2 ATP to modify glucose molecule split into 2 phosphorylated 3 carbon molecules called glyceraldehyde 3-phosphate
energy investment phase (glycolysis)
energy investment of 2 ATP to modify glucose molecule split into 2 phosphorylated 3 carbon molecules called glyceraldehyde 3-phosphate
energy payoff phase (glycolysis)
oxidizes glyceraldehyde 3-phosphate into two pyruvate, producing 4 ATP and reducing 2 NAD+ to NADH, using electrons that originated from glucose
substrate level phosphorylation
how ATP produces by glycolysis and kreb’s cycle are formed. phosphate group is removed from an organic molecule and directly transferred to ADP molecule, making ATP
products of glycolysis
4 ATP (2 net gain), 2 NADH (goes to electron transport chain), and 2 pyruvate (goes to krebs/transition stage)
glycolysis location
occurs in cytoplasm
transition reaction
pyruvate must be converted to a 2-carbon acetyl group to enter kreb’s cycle. Pyruvate becomes coenzyme A (CoA)
products of transition reaction
(for two pyruvates) 2 CoA, 2 NADH, 2 CO2
transition reaction location
occurs in mitochondrial matrix of eukaryotes; cytoplasm of prokaryotes
Kreb’s cycle
8 step cycle that transfers the remaining electrons from acetyl group to electron carrier molecules, thus reducing them
Kreb’s cycle products
2 ATP, 4 CO2, 6 NADH, 2 FADH2
Kreb’s cycle location
mitochondrial matrix in eukaryotes; cytoplasm in prokaryotes
cellular respiration
process of producing ATP, begins when electrons are transferred from carriers through a series of chemical reactions to a final inorganic electron acceptor
electron transport system
last component involved in cellular respiration; it is a series of chemical reactions in that electrons from NADH and FADH2 are passed rapidly from one ETS electron carrier to the next
redox potential
for a protein or chemical to accept electrons, it must have a more positive redox potential than its electron donor. electrons move from carriers w/ more negative redox potential to those w/ more positive redox potential
aerobic respiration
uses oxygen as its final electron acceptor that becomes reduced to water (H2O)
anaerobic respiration
uses a different inorganic molecule as its final electron acceptor (nitrite, nitrate, carbonate, sulfate) and less ATP is formed through anaerobic respiration compared to aerobic
proton motive force
the ETS creates an uneven distribution of protons across the membrane and forms an electrochemical gradient known as the proton motive force
oxidative phophorylation
creates ATP using the potential energy from the PMF through ATP synthase
ATP synthase
H+ ions diffuse across membrane through ATP synthase, which acts as a generator and generates ATP from ADP harnessing the energy from the protons moving through
Electron transport system products
6 H2O, 34 ATP
Yield of ATP from aerobic respiration
2 ATP from glycolysis, 2 ATP from Kreb’s cycle, 34 ATP from oxidative phosphorylation
Yield of ATP from anaerobic respiration
2 ATP from glycolysis, 2 ATP from kreb’s, 1-32 ATP from oxidative phosphorylation
reasons why some cells cannot respirate
cells lack sufficient amount of inorganic final electron acceptor, cell lacks genes to make appropriate complexes and electron carriers, cell lacks genes to make one or more enzymes in the kreb’s cycle
fermentation
the purpose of fermentation is to ensure an adequate supply of NAD+ for glycolysis so the cell can produce energy
lactic acid fermentation
pyruvate + NADH -> lactic acid + NAD+
produces lactic acid as byproduct of producing NAD+ for glycolysis
lactic acid fermentation equation
C6H12O6 -> 2CH3CH(OH)COOH + energy (2 ATP)
alcohol fermentation
creates ethanol as byproduct of producing NAD+ for glycolysis
alcohol fermentation equation
C6H12O6 -> 2CH3CH2OH + 2 CO2 + energy (2 ATP)
different fermentation products
fermentation products depend on requirements of organism and their DNA. microbes can be differentiated according to the substrates they ferment
photoautotroph
get their energy from light and use an inorganic carbon sourse
chemoautotroph
get their energy from chemicals and use an inorganic carbon source
photoheterotroph
get their energy from light and use an organic carbon source
chemoheterotroph
get their energy from chemical and use an organic carbon source
