Exam 1 Study Guide Flashcards
Chapters 1-5, 7
List the top three cause of death in the US. Describe how the role of microbes has changed in the last 100 years.
- Heart diseases
- Cancer
- stroke
- In the last 100 years, microbes used to be the main cause of death, but now, because of clean water and no sewage contamination, vaccination, discovery of antibiotics by Alexander Flemming
what were the first living creatures on planet earth?
- microbes are the first living creatures on planet earth
- microbes are more diverse than plants and animals
- more abundant than any other living thing
where do microbes grow?
- in every ecological niche on earth that has a source of liquid H2O
what effect do microbes have on the environment?
- they can transform the geosphere
- Can affect the climate by production/use of CO2, N2, O2, and CH4
- Participate in symbiotic relationships with other organisms
what are microbes involvement in diseases?
- only a small fraction of microbes cause diseases
- diseases caused by microbes are called “infectious diseases”
where in the human body can bacteria be found?
- colonization can only occur at body sites that provide nutrients and the right environment for the microbes to flourish
- can live stably in/on the human body
when do microbiota start to collect in the human body and how long do they stay?
- begin to acquire as newborns
- may colonize the body indefinitely
- may colonize the body fleetingly
how does microbiota help the body?
- normal microbiotas prevent growth of pathogens
- normal microbiotas produce growth factors such as vitamins B and K
- may help train the immune system to discriminate threats
swan-neck flask experiments
Louis Pasteur had swan-neck flasks that once the solution was boiled within them, no new growth occurred. But, if they were broken, then microbial growth did occur. He learned that no new growth occurred was because all the dust and germs from the air were trapped in the neck instead of in the solution. This helped to develop a new way to keep solutions sterile.
disproved theory of spontaneous generation
- Spontaneous generation: living organisms could develop from nonliving matter
- Challenged multiple times: Francesco Redi in covering meat; when they were covered, no maggots, when they were open, there were maggots.
- Lazzaro Spallanzani: boiling water in a flask prevented microbial growth, concluded that germs must be in the air
- Swan-neck experiments
- John Tyndall & Ferdinand Cohn: broth was sterile even when exposed to air, proved that dust had germs in it
yeast fermentation to make alcohol
- Louis Pasteur proved that fermentations were carried out by living organisms and not by the degradation of sugars from chemical instability
- Specific yeasts and bacteria have to do with fermentation
- Beet sugars: yeast was replaced with bacteria
- Wine in France: contamination of wines by other microbes
pasteurization
Developed by Louis Pasteur, used to heat liquids to destroy microbes, found out when he consulted the wine industry in France
Louis Pasteur
Trained as a chemist, contributed much to the world of microbiology, Developed pasteurization, discovered fermentation was done by specific yeasts and bacteria, developed a vaccine after discovering attenuated bacteria could not cause disease and developed the anthrax and rabies vaccines, and disproved spontaneous generation through the swan-neck experiments
Antony van Leeuwenhoek
In 1673, he constructed simple microscopes composed of double convex glass lenses held between two silver plates. These microscopes could magnify 50-300 times and illuminated them by shining a light at a 45 degree angle of the specimen plane (dark field illumination).
Edward Jenner
Pasteur named attenuated bacteria a vaccine (vacca meaning cow) after Jenner because he used material from cowpox lesions to protect people against smallpox.
Ignaz Semmelweis
First person to realize that a pathogen could be transmitted from one person to another (1847-1848). Found that doctors and medical students were infecting pregnant women with fluids from other procedures due to a lack of hand washing. Pioneer of antisepsis in obstetrics.
Robert Koch
- Developed the first demonstration that bacteria can cause disease, mycobacterium tuberculosis can cause TB, developed pure culture methods using agar,
- Developed Koch’s postulates
etiology of anthrax
- The first direct demonstration that bacteria could cause disease came from Koch’s study of anthrax, realizing that Bacillus anthracis caused anthrax outbreaks
- Pasteur and Chamberland later developed a vaccine for it
what are Koch’s postulates
- The microorganism must be present in every case of the disease but absent from healthy organisms
- The suspected microorganisms must be isolated and grown in a pure culture
- The same disease must result when the isolated microorganism is inoculated into a healthy host
- The same microorganism must be isolated again from the diseased host
John Snow
- Discovered the cause of cholera was from unwashed hands and shared foods and not by bad air. Also found that the Broad street pump was contaminated, which was causing people to get the disease.
Alexander Flemming
- In 1929, he rediscovered the fungus penicillium that produced penicillin. It was the first antibiotic that could successfully control bacterial infections
- It was mass produced by WW 2
Paul Ehrlich
- father of antibiotics
- developed arsenic based medication for syphilis
define cell
- the smallest structural and functional unit of an organisms, typically microscopic and consisting of cytoplasm and nucleus enclosed in a membrane, can be eukaryotic or prokaryotic
- Made of molecules, those molecules are used to create structure, and that structure performs a function
define microbe
entities that cannot be seen with the naked eye
- need magnification to see them
what are the hallmarks of the cell?
- be able to replicate itself
- source of energy
- control the flow of chemicals (cell membrane)
- DNA as the primary genetic material (not only RNA)
what are prions?
An infectious agent consisting only of proteins; prions cause a variety of spongiform encephalopathies such as scrapie in sheep, acellular
what are virions?
Simple virus particles, composed only of proteins and a nucleic acid and can be extremely small, acellular
what are viruses?
An infectious agent having a simple acellular organization with a protein coat and a nucleic acid genome, lacking independent metabolism, and multiplying only within living host cells
what kingdoms and domain are a part of prokaryotes?
domain: Bacteria
kingdoms: bacteria and archaebacteria
- monera is a kingdom with the other 5
what kingdoms and domain are a part of eukaryotes?
kingdoms: plant, animal, protist, and fungi
domain: eukarya
what are the six major bio-elements?
- carbon
- hydrogen
- oxygen
- nitrogen
- phosphorous
- sulfur
besides the 6 major bio-elements, what other elements are important to life?
magnesium, zinc, iron, sodium, and potassium
which bio-elements form carbohydrates?
sugars are made up of CHO
which bio-elements form lipids?
fatty acids and glycerol are made up of CHO
which bio-elements form nucleic acids?
nucleotides are made up of CHONP
which bio-elements form proteins?
amino acids are made up of CHONS
define magnification
- power of the lens
- calculated by multiplying the objective and eyepiece magnifications together
define refractive index
how the structure in the microscope slide bent the light
define resolution
- how clear the specimen is
- the ability of a microscope to distinguish between small objects that are close together.
- just because there is a higher magnification doesn’t mean that the resolution is clear
what is the purpose of oil immersion?
Used to increase the total magnification power of a microscope because oil has a high refractive index, therefore increasing the aperture of the objective lens
define smear preparation (role of heat fixation)
a smear is a film of cells, in heat fixation, this process is used to observe bacteria and archaea. The process preserves overall morphology and inactivates enzymes, but destroys proteins and subcellular structures
what is the role of microbes in maintaining temperature on earth? (role of microbes in CO2 and CH4 recycling?)
- Cyanobacteria were the first organisms to release oxygen in abundance into the atmosphere
- Only bacteria can fix nitrogen
- Microbes are important in fixing carbon
- It plays a role in producing and removing greenhouse gases like CO2 and CH4
- They could be used to remove pollution
what membrane-bound organelles are present in eukaryotes but not in prokaryotes?
mitochondria/chloroplasts, lysosome, golgi aparatus, and endoplasmic reticulum
compare prokaryotes and eukaryotes on the presence and makeup of cell wall
- Prokaryotes have a rigid cell wall, in eukaryotic organisms, vertebrates don’t have cell walls but plants do
- cell walls in prokaryotes are made of peptidoglycan, some eukaryotic cell walls are made of cellulose or chitin
compare the prokaryotes and eukaryotes on the presence of organelles
- In eukaryotic organisms, organelles are membrane bound while prokaryotic organisms have free organelles.
- Prokaryotes also lack some internal structures that are in eukaryotes like the endoplasmic reticulum and the Golgi apparatus
compare the prokaryotes and eukaryotes on their chromosomes structure and organization
- Eukaryotes have double stranded linear DNA and prokaryotes have double stranded circular DNA. Eukaryotes have mitochondrial DNA with histones and prokaryotes use plasmids
ionic bond
most atoms have less electrons than protons, so they carry either a positive or negative ion. Cations are positive and anion carries a negative charge. When a cation and anion approach each other, they are attracted by their opposite charges. This ionic attraction that holds two groups together is an ionic bond
covalent bond
- are joined together by sharing pairs of electrons.
- If electrons are equally shared between identical atoms, the covalent bond is strong and non-polar
- If there are two different atoms, the covalent bond formed is polar because the electrons are pulled toward the more electronegative atom
- strongest bond
hydrogen bond
- when a hydrogen atom is covalently bonded to a more electronegative atom such as oxygen or nitrogen, the electrons are unequally shared and the hydrogen atom carries a partial positive charge.
- Although hydrogen bonds are weak, there are so many in proteins and nucleic acids that they play a major role in determining protein and nucleic acid structure
hydrophobic interaction
a nonpolar substance lacking affinity for water (or which is not readily soluble in water)
what is the role of water in biological activities?
- H bonds between water molecules contribute to high BP
- H bonds hold and absorb energy making water a temperature buffer
- Water is a polar molecule and capable of forming H bonds with others, this makes water an excellent solvent
define water activity (Aw)
a quantitative measure of water availability in the habitat; the water activity of a solution is one-hundredths its relative humidity
define osmosis
when two solutions are separated by a semipermeable membrane that allows movement of water but not solutes.
define osmolarity
solute concentration
define osmotolerant
organisms that grow over a fairly wide range of water activity or solute concentration
define halophiles and explain why they survive in their environment
- like high concentrations of salt
- They can live in these extreme conditions because they synthesize or obtain from their environment molecules called compatible solutes. Compatible solutes can be kept at high intracellular concentrations without interfering with metabolism or growth
what is the difference between endergonic and exergonic reactions?
- An endergonic reaction is a reaction that does not spontaneously go to completion as written; the standard free energy change is positive and the equilibrium constant is less than one; requires energy
- An exergonic reaction is a reaction that spontaneously goes to completion as written, the standard free energy change is negative, and the equilibrium constant is greater than one; releases energy
what is the difference between hydrolysis and dehydration?
- hydrolysis: bonds are broken and a water molecule is added
- Dehydration: bonds are formed and a water molecule is lost, synthetic reaction
what is the difference between hydrolytic and condensation reactions?
Condensation involves the formation of a new chemical bond while hydrolysis involves the breakdown of a chemical bond
Define folding and denaturation of protein molecules.
if a protein is altered so severely that the protein no longer functions, the protein is said to be denatured
what are the factors that affect protein shape?
- pH
- temperature
- salt concentration
- changing these variables alters the activity/function of a protein
what are the different levels of protein folding? What kind of bonds are associated with each level?
- Primary structure: hydrogen and peptide bonds
- Secondary structure: hydrogen and peptide bonds
- Tertiary structure: hydrogen, peptide, disulfide bridges, hydrophobic interactions
- Quaternary structure; van der Waals forces, hydrogen, peptide, disulfide bridges
define an amphipathic molecule
An amphipathic molecule is a molecule that has both hydrophobic and hydrophilic regions. One example of this could by phospholipids
basic dyes
have positively charged groups, bind to negatively charged molecules such as nucleic acids, many proteins and the surfaces of bacterial and archaeal cells
acidic dyes
have negatively charged groups; bind to positively charged cell structures
negative staining
a staining procedure in which dye is used to make the background dark while the specimen is unstained, uses acidic dye that binds to the background, india ink
positive staining
uses basic dye that binds to the specimen, CV
simple stain
employs a basic dye to impart a color to a cell. Easy way to increase the contrast between otherwise colorless cells and a transparent background; uses one stain to show morphology, size, and arrangement
differential stain
distinguishes one group of organisms from another
gram stain
used to separate bacteria into two major groups, gram-positive and gram-negative. The staining characteristics of these groups reflect a fundamental difference in the chemical structure of their cell walls. This is the most widely used staining technique
acid-fast stain
used to detect members of the genus mycobacterium in a specimen, due to the lipid composition of their cell walls, these organisms do not readily take up stains
special stains
stains specific structures inside or outside of a cell
capsule stain
because the viscous capsule does not readily take up stains, it stands out against a stained background, example of a negative stain
endospore stain
stains endospores, a type of dormant cell that does not readily take up stains. These are produced by the genera Bacillus and Clostridium
flagella stain
the staining agent adheres to and coats the otherwise thin flagella, enabling them to be seen with the light microscope
fluorescent dyes and tags
fluorescent dyes and tags absorb ultraviolet light and then emit light of a longer wavelength. They are used in conjunction with a fluorescence microscope
fluorescent dyes
some fluorescent dyes bind to compounds found in all cells, others bind to compounds specific to only certain types of cells
fluorescent tags
antibodies to which a fluorescent molecule has been attached are used t tag specific molecules
What are the three medical important structures present in bacteria?
capsule, endospore, and flagella
define and describe the importance of wet mount
• Wet mount: bacterium in a drop of water. The refractive indices of bacterial cell structures are greater than that other water, therefore light passes through the cell structure will refract, showing the structure of the cell
explain the steps involved in gram staining procedure
- Step 1: crystal violet (primary stain) for 1 minute, water rinse – cells stain purple
- Step 2: iodine (mordant) for 1 minute, water rinse – cells remain purple
- Step 3: alcohol (decolorizer) for 10-30 seconds, water rinse – gram positive cells remain purple, gram-negative cells become colorless
- Step 4: safranin (counterstain) for 30-60 seconds, water rinse, blot dry – gram positive cells remain purple, gram-negative cells appear red
What is the significance of acid-fast staining procedure?`
- It is used to identify mycobacterium tuberculosis and M. leprae, the pathogens responsible for tuberculosis and leprosy
- These bacteria, as well as other mycobacteria, have cell walls containing lipids constructed from mycolic acids, a group of branched-chain hydroxy fatty acids, which prevent dyes from readily binding to the cells
Which microscope uses the differences in refractive index and cell density to visualize live cells?
phase-contrast microscopes
plasma membrane
selectively permeable barrier, mechanical boundary of the cell, nutrient and waste transport, location of many metabolic processes (respiration and photosynthesis), detection of environmental cues for chemotaxis
gas vacuole
buoyancy for floating in aquatic environments
inclusions
storage of carbon, phosphate, and other substances
periplasmic space
- in typical gram-negative bacteria, contains hydrolytic enzymes and binding proteins for nutrient processing and uptake, in typical gram-positive bacteria, may be smaller or absent
ribosomes
protein synthesis
nucleoid
localization of genetic material (DNA)
cell wall
gives prokaryotes shape and protection from osmotic stress
capsules and slime layers
resistance to phagocytosis, adherence to surfaces
fimbriae and pili
attachment to surfaces, bacterial mating
flagella
movement
endospore
survival under harsh environmental conditions
what is the significance of periplasmic space?
- The space between the plasma membrane and the outer membrane in typical gram-negative bacteria, and between the plasma membrane and the cell wall in typical gram-positive bacteria.
- Contains hydrolytic enzymes and binding proteins for nutrient processing and uptake
- One of the areas used for synthesis of peptidoglycan (also in cytoplasm and plasma membrane)
glycocalyx
network of polysaccharides extending from the surface of the cell. a capsule or slime layer composed of polysaccharides can also be referred to as a glycocalyx
capsule
usually composed of polysaccharides; well organized and not easily removed from cell
S layer
regularly structured layers of protein or glycoprotein. More common among Archaea (protects against osmotic stress)
Pili
similar to fimbriae except longer, thicker, and less numerous (1-10/cell)–required for mating
fimbriae
short, thin, hairlike, proteinaceous appendages up to 1,000/cell–mediate attachment to surfaces–some (type IV fimbriae) required for twitching motility or gliding motility that occurs in some bacteria
bacterial flagella
- flagellum rotates like a propeller
- Counterclockwise rotation causes forward motion (run)
- Clockwise rotation disrupts run causing a tumble (tumble)
What is bacterial flagella’s role in chemotaxis?
- Motility is used to move toward nutrients such as sugars and amino acids from many harmful substances and bacterial waste products
- Participates in the movement towards chemical attractants and away from repellents
- Can also move in response of environmental cues like temp (thermotaxis), light (phototaxis), oxygen (aerotaxis), osmotic pressure (osmotaxis), and gravity
ribosomes in bacteria
intimately involved in protein synthesis, two subunits 30S and 50S join to form the 70S ribosome, which serves as the structure that facilitates the joining of amino acids
plasmids in bacteria
carries genetic information that may be advantageous to a cell in certain situations
filamentous appendages
: composed of subunits of proteins that form a helical chain
sheath
protect aquatic bacteria from disruption by turbulent waters
cytoplastic membrane
phospholipid bilayer embedded with proteins, a barrier between the cytoplasm and the outside environment. Also functions as a discriminating conduit between the cell and its surroundings
chromosomal DNA in prokaryotes
carries the genetic information that is essential to a cell. Typically a single, circular, double-stranded DNA molecule
granules
accumulations of high molecular weight polymers which are synthesized from a nutrient that a cell has in relative excess
colony
visible growth or cluster of microorganisms
pure culture
population of cells arising from a single cell
streak
- a petri dish of solid culture medium with isolated microbial colonies growing on its surface that has been prepared by spreading a microbial mixture over the agar surface, using an inoculating loop
- Cells are transferred to the edge of an agar plate with an inoculating loop or swab and then streaked across the surface in one of several patterns
spread
a petri dish of solid culture medium with isolated microbial colonies growing on its surface that has been prepared by spreading a dilute microbial suspension evenly over the agar surface
- A small volume of diluted mixture containing around 25-250 cells is transferred to the center of an agar plate and spread evenly over the surface with a sterile bent rod. The dispersed cells develop into isolated colonies
pour plate
- a petri dish of solid culture medium with isolated microbial colonies growing both on its surface and within the medium that has been prepared by mixing microorganisms with cooled, still-liquid medium and then allowing the medium to harden
- Used with bacteria, archaea, and fungi
- Used for microbes that outgrow the streak and spread methods
- In this method, the original sample is serially diluted to reduce the microbial population to obtain separate colonies when plating. Small volumes of several diluted samples are mixed with liquid agar that has been cooled to 45 C and poured into sterile dishes. Become fixed in the agar after it hardens and incbates
turbidity
cell density in a culture sample
absorption
the measure of the amount of light absorbed by suspension of bacterial cells or a solution
optical density
the extent of light scattering can be measured by a spectrometer and is called the absorbance of the medium
binary fission
- asexual reproduction in which a cell separates into two identical daughter cells
- Most bacterial and archaeal cells reproduce this way
what are the different kinds of light microscopes?
o Bright-field o Phase-contrast o Interference o Dark-field o Florescence o Confocal microscope
what are the different kinds of electron microscopes?
o Transmission electron microscopes (TEM)
o Scanning electron microscopes (SEM)
what are the different kinds of scanning probe microscopes?
- scanning tunneling
- atomic force
Compare light microscopy and electron microscopy based on highest practical magnification, best resolution, and radiation source.
- Highest practical magnification: 1,00-1500 in LM, over 100,000 in EM
- Best resolution: .2 mm in LM, .5 nm in EM
- Radiation source: visible light in LM, electron beam in EM
confocal scanning laser microscopy
- Confocal scanning laser microscopy uses computer integration of images from many different focal planes to generate 3-D pictures
- Usually fluorescent dyes attached to antibodies are used in conjunction with laser light source to produce sharp images
Define Fluorescent microscope and determine where its source of illumination comes from
- A microscope that exposes a specimen to light of a specific wavelength and then forms an image from the fluorescent light produced.
- Fluorescent light
why is the Gram staining procedure is not appropriate for staining mycobacteria?
Have cell walls containing lipids constructed from mycolic acids that prevent dyes from readily binding to cells
what staining procedure is used to stain for mycobacteria?
acid-fast staining
Extremophiles such as microbes found in hot springs in Yellowstone National Park are most likely members of ___________ domain
- archaea
- extremophiles
which structure in a cell determines its morphology?
cell wall
what are the bacterial morphology types?
form, elevation, and margin
cocci
roughly spherical bacterial or archaeal cell
diplococci
a pair of cocci
bacilli
a rod shaped bacterial cell
spirilla
rigid, spiral-shape cells
spirochetes
a flexible, spiral-shaped bacteria with periplasmic flagella
pleomorphic
refers to cells or viruses that are variable in shape and lack a single, characteristic form
selective media
culture media that favor the growth of specific microorganisms, this may be accomplished by inhibiting the growth of undesired microorganisms
differential media
culture media that distinguishes between groups of microorganisms based on differences in their growth and metabolic products
blood agar
enriched and differential; Blood agar supports the growth of many fastidious bacteria. These can be differentiated based on their ability to produce hemolysins—proteins that lyse red blood cells. Hemolysis appears as a clear zone (β-hemolysis) or greenish halo around the colony (α-hemolysis) (e.g., Streptococcus pyogenes, a β-hemolytic streptococcus)
eosin methylene blue (EMB) agar
selective and differential; Two dyes, eosin Y and methylene blue, inhibit the growth of Gram-positive bacteria. They also react with acidic products released by certain Gram-negative bacteria when they use lactose or sucrose as carbon and energy sources. Colonies of Gram-negative bacteria that produce large amounts of acidic products have a green, metallic sheen (e.g., fecal bacteria such as E. coli).
MacConkey (MAC) agar
selective and differential; The selective components in MAC are bile salts and crystal violet, which inhibit the growth of Gram-positive bacteria. The presence of lactose and neutral red, a pH indicator, allows the differentiation of Gram-negative bacteria based on the products released when they use lactose as a carbon and energy source. The colonies of those that release acidic products are red (e.g., E. coli).
Mannitol sugar agar
selective and differential; A concentration of 7.5% NaCl selects for the growth of staphylococci. Pathogenic staphylococci can be differentiated based on the release of acidic products when they use mannitol as a carbon and energy source. The acidic products cause a pH indicator (phenol red) in the medium to turn yellow (e.g., Staphylococcus aureus).
What was the differences between spontaneous generation and germ theory of disease?
Spontaneous generation is the idea that matter arises from nothing, while the germ theory of disease is the idea that diseases arise from microorganisms, one has causation and the other does not
Define Oligotrophic Environments. How microbes respond to them?
- Oligotrophic Environments: an environment containing low levels of nutrients that support microbial growth
- Microbes respond to this environment by producing endospores, become dormant, or form cysts
- Many in this environment live in a state of growth arrest, cell division is halted to conserve ATP, storage inclusions are used for nutrients, will decrease in size
Define pleomorphic
refers to cells or viruses that are variable in shape and lack a single, characteristic form
Define mycelium
a mass branching hyphae found in fungi and some bacteria
Define PHB
poly-B-hydroxybutyrate, a linear polymer of B-hydroxybutyrate used as a reserve of carbon and energy by many bacteria; PHB granules are surrounded by a single-layered shell composed of protein, studied in the use of biodegradable plastics
Define PTS
- sugar phosphotransferase system, A group translocation system used by many bacteria. As a sugar is transported into the cell, the hydrolysis of a high-energy phosphate bond fuels its import, and the sugar is modified by the covalent attachment of the phosphoryl group.
- Observed in bacteria, transports a variety of sugars while phosphorylating them, using PEP ad the phosphate donor
Define ABC transport system
Transport systems that use ATP hydrolysis to drive translocation across the plasma membrane; can be used for nutrient uptake (ABC importer) or export of substances (ABC exporter), including protein secretion (ABC protein secretion pathway)
Define biofilm
Organized microbial communities encased in extracellular polymeric substances and associated with surfaces, often with complex structural and functional characteristics
Define quorum sensing
The process in which bacteria monitor their own population density or the presence of other species of bacteria by sensing the levels of signal molecules (e.g., N-acylhomoserine lactone) released by the microorganisms. When these signal molecules reach a threshold concentration, quorum-dependent genes are expressed.
compare makeup of the plasma membrane of bacteria and archaea
- Bacteria: Ester-linked phospholipids form a lipid bilayer
- Archaea: Glycerol diethers form lipid bilayers; glycerol tetraethers form lipid monolayers
compare the cell wall constituents of bacteria and archaea
- Bacteria: Peptidoglycan is present in nearly all; some lack cell walls
- Archaea: Very diverse but peptidoglycan is always absent: some consist of S-layer only, others combine S-layer with polysaccharides or proteins or both; some lack cell walls
compare the inclusions present of bacteria and archaea
bacteria and archaea: yes, including gas vacuoles
compare the ribosomes of bacteria and archaea
both are 70S
compare the chromosome structure of bacteria and archaea
- Bacteria: Most are circular, double-stranded (ds) DNA
- Archaea: All known are circular, dsDNA
compare the plasmid presence of bacteria and archaea
- Bacteria: Yes; circular and linear dsDNA
- Archaea: yes; circular dsDNA
compare the external structures of bacteria and archaea
- Bacteria: Flagella, fimbriae (pili) common
- Archaea: Archaella, pili common
compare the capsules/slime layers of bacteria and archaea
- Bacteria: common
- Archaea: rare
compare the three domains on true-membrane bound organelles
- Bacteria and archaea: no
- Eukaryotes: yes
compare the three domains on their DNA complex with histones
- Bacteria: no
- Archaea: some
- Eukaryotes: yes
compare the three domains on their chromosomes
- Bacteria: Usually one circular chromosome; chromosomes have single origin of replication; some are polyploid
- Archaea: One circular chromosome; some have chromosomes with multiple origins of replication; some are polyploid
- Eukaryotes: Multiple, linear chromosomes with multiple origins of replication
compare the three domains on their plasmids
- bacteria and archaea: very common
eukaryotes: rare
compare the three domains on their introns in the genes
- bacteria and archaea: no
- eukaryotes: yes
compare the three domains on their nucleus
- bacteria and archaea: no
- eukaryotes: yes
compare the three domains on mitochondria, endoplasmic reticulum, golgi, and lysosomes observed
- bacteria and archaea: no
- eukaryotes: yes
compare the three domains on flagella
- Bacteria: Submicroscopic in size; filament composed of single type of flagellin protein
- Archaea: Submicroscopic in size; some filaments composed of more than one type of archaellin protein
- Eukaryotes: Microscopic in size; membrane bound; usually 20 microtubules in 9 + 2 pattern
compare the three domains on peptidoglycan in their cell walls
- bacteria: yes
- eukaryotes and archaea: no
compare the three domains on cytoskeletons
- bacteria and archaea: rudimentary
- eukaryotes: no
compare the three domains on gas vesicles
- bacteria and archaea: yes
- eukaryotes: no
what is the difference between pili and cilia?
- Pili: A fine, hairlike protein appendage on many bacteria, archaea, and some fungi. They attach cells to surfaces, and some are involved in twitching motility.
- Cilia: Threadlike appendages extending from the surface of some protists that beat rhythmically to propel them; cilia are membrane-bound cylinders with a complex internal array of microtubules, usually in a 9 + 2 pattern.
List the top 3 causes of death in the US
- heart diseases
- cancer
- stroke
List effects of microbes on ecosystem. List extreme conditions at which microbes can thrive
Microbes exist in any kind of ecosystem, and without them, there would not be any ecosystems; microbes can live in areas with low or high pH, different types of solutes at different concentrations (halophiles), hot or cold temperatures, with or without oxygen, at high pressures, and at high radiation levels.
what is the role of enzymes in chemical reactions?
- Catalyze chemical reactions
- They lower the activation energy for the reaction to begin
What is a typical gram-positive cell envelope?
Cell wall, a thick layer of peptidoglycan, and then the plasma membrane
What is a typical gram-negative cell envelope?
Cell wall, outer membrane, thin layer of peptidoglycan, periplasmic space, and then the plasma membrane
what is the importance of bacterial cell membrane?
The plasma membrane encompasses the cytoplasm and defines the cell, if it is removed then the cell is compromised and the contents would likely spill into the environment, causing it to die. It is also responsible for the cell’s interaction with outside environments
What are steroids? Give examples. What is their role in function of cell membranes?
- Steroids are a class of organic compounds with a characteristic molecular structure consisting of four rings of carbon atoms.
- Steroid hormones act as a signaling molecules in the body.
- A subgroup of steroids are sterols, which includes cholesterol- a molecule that reduces the fluidity of the cell membrane and is a precursor to fat-soluble vitamins and steroid hormones.
what are hopanoids?
- Lipids found in bacterial membranes that are similar in structure and function to the sterols found in eukaryotic membranes.
simple diffusion
- also called passive diffusion, The movement of molecules from a region of higher concentration to one of lower concentration as a result of random thermal agitation.
- Most substances can’t freely move into a cell; the only ones that move through facilitated diffusion is water and a few gases like O2 and CO2
facilitated diffusion
- Diffusion across the plasma membrane that is aided by a channel protein or a carrier protein
- The rate of facilitated diffusion increases with the concentration more rapidly at lower concentrations of the diffusion molecule than passive diffusion
- Carrier proteins are more substrate specific than channel proteins
Active transport
The transport of solute molecules across a membrane against a gradient; it requires a carrier protein and the input of energy. Three major types are primary active transport, which uses hydrolysis of ATP to power transport; secondary active transport, which uses ion gradients across a membrane to power active transport; and group translocation
primary active transport
use energy provided by ATP hydrolysis to move substance against a concentration gradient without modifying them. Use uniporters to move molecules, specifically ABC transporters
secondary active transport
couples the potential energy of ion gradients to transport of substance without modifying them. They are cotransporters. Uses symport and antiport.
group translocation
An active transport process in which a molecule is moved across a membrane by carrier proteins while being chemically altered at the same time (e.g., phosphoenolpyruvate: sugar phosphotransferase system).
uniport
Carrier proteins that move a single solute across a membrane
symport
Linked transport of two substances across a plasma membrane in the same direction
antiport
Coupled transport of two molecules in which one molecule enters the cell as the other leaves the cell
fluid mosaic model
the model of cell membranes in which the membrane is a lipid bilayer with integral proteins buried in the lipid and peripheral proteins more loosely attached to the membrane surface
semi-permeable
allow particular ions and molecules to pass either into or out of the cell, while preventing the movement of others
Semi-permeable and fluid mosaic model refer to which structure?
plasma membrane
List cardinal temperatures of growth. Which group is readily isolated from arctic and Antarctic?
- minimum, optimum, and maximum
- psychophiles
List three medically important structures viewed by structural staining processes.
endospores, capsules, and flagella
what are the important features of endospores
- Very resistant to environmental stressors – this is due to a core being surrounded by several layers with all different compositions
- Many are dangerous pathogens
sporulation
the process of spore formation
germination
The stage following spore activation in which the spore breaks its dormant state. Germination is followed by outgrowth
vegetative life
normal, continuous cycle of growth and division; activation, germination, and outgrowth
what types of bacteria make endospores?
Clostridium, sporosarcina, bacillus, and Firmicutes
What are some significant diseases caused by bacteria that produce endospores?
- Clostridium botulinum causes botulism, a food-borne disease that results from ingestion of botulinum toxin, the deadliest toxin known
- B. anthracis: causes anthrax
- C. tetani: causes tetanus
- C. perfringens: causes gas gangrene and food poisoning
what are the four major polymers
Polysaccharides, lipids, nucleic acids, and proteins
What are the building blocks (monomer) of polysaccharides?
sugars
What is the function of polysaccharides?
- Contribute to structural support
- Serve as nutrient and energy stores
- Important components of cell membrane
where are polysaccharides found in the cell?
- Cellulose: found in plants and algae
- Peptidoglycan: found in bacterial cell walls
- Lipopolysaccharides: complex of lipid and polysaccharide (endotoxins)
- Glycocalyx: found on outer surfaces, functions in attachment, and has a role in biofilm
what bonds are associated with polysaccharides?
glyosidic bonds
what are the building blocks of lipids?
fatty acids as the tail, glycerol as the head
what is the function of lipids?
- control what comes into and out of the cell
- makes membranes
- protein attachment
what kind of bonds hold lipids together?
ester bonds
where can lipids be found in the cell?
cell membrane
what are the building blocks of nucleic acids?
- nucleotides
what kind of bond holds monomers of nucleic acids together?
phosphodiester bonds
what are the functions of nucleic acids?
DNA is genetic material
- RNA is also genetic material, but functions as other communications like tRNA or rRNA
where can nucleic acids be found?
- in all cells, nucleus/nucleoid
what are the building blocks of proteins?
amino acids
- proteins are the most abundant polymer in the body
what are the functions of proteins?
- Enzymes catalyze chemical reactions
- Regulate cellular processes
- Provide structural support
- Surface receptors
- As carriers
what kind of bonds hold amino acids together?
- Primary: peptide bonds and hydrogen bonds
- Secondary: hydrogen and peptide
- Tertiary: hydrogen, peptide, disulfide bridges, hydrophobic interactions
- Quaternary: hydrogen, peptide, disulfide bridges, hydrophobic interactions, Van der Waals
Describe Van der Waals forces
- no direct interaction
- holds positive and negative bonds in a stable interaction
- play a role in structure (especially in quaternary protein structures)
How does magnesium, zinc, iron, sodium, and potassium play in microorganisms?
mg: protein structure
zinc and iron: stabilize protein structure
Na and K: pumping materials across the membrane
Define the importance of the interaction between ligand and receptor molecules
a ligand is something outside of the cell that interacts with the outside of the cell through a receptor. Ligands are typically horomones, antibodies, and enzymes. Bacteria and viruses take advantage of this process, which is how they get us sick
how is the cell wall affected by penicillin and lysozyme?
- Lysozyme attacks peptidoglycan by hydrolyzing the bond that connects NAM and NAG
- Penicillin inhibits the enzyme responsible for building peptidoglycan chains, called transpeptidase
- If in a hypotonic solution, they lyse
Define the primary producers and give examples. What are the Carbon, Energy and Electron sources for photolithoautotrophs and chemolithoautotrophs. Give examples
- Primary producers: they fix CO2, making reduced organic molecules that sustain chemoorganohetertrophs that share their habitats
- Photolithoautotrophs get carbon from CO2, energy from light and electron from inorganic electron donor, examples would be cyanobacteria, diatoms, and sulfur bacteria
- Chemolithoautotrophs get carbon from CO2, energy from inorganic chemicals, electrons from inorganic electron donor, and examples of this would be sulfur-oxidizing bacteria, hydrogen oxidizing bacteria, methanogens
what are the 5 stages of bacterial growth curve?
Lag phase, exponential phase, stationary phase, death phase, and long-term stationary phase
What events happen in the 5 stages of the growth curve?
- Lag phase is synthesizing new components, like making ATP, cofactors and ribosomes, or it may need to repair itself and replicate DNA. It is not inactivity
- Exponential is when the rate of growth is at its highest
- Stationary phase is when the growth curve is horizontal and the amount of organisms is constant. May cease to divide but remain metabolically active. Enter this stage because nutrients are limited or O2
- Death phase is the number of viable cells decrease at a constant rate, buildup of toxic waste and nutrient deprivation
- Long term stationary phase: can last months or years, survival of the fittest, reproducing cells and nonviable cells die off
Define generation time and which stage it is calculated from.
- The time required for a microbial population to double in number.
- Calculated off of the exponential phase
List and describe the influence of environmental factors on microbial growth
Solute concentration and water activity, pH, temperature, oxygen concentration, pressure, and radiation
list and describe oxygen requirements for bacterial growth
- Obligate anaerobe: has to grow in the presence of oxygen
- Facultative anaerobe: does not require O2, but grows better in it
- Aerotolerant anaerobe: can grow with or without oxygen
- Obligate anaerobe: cannot grow in oxygen
- Microaerophile: requires oxygen between 2-10%, dies above 20%
What is the significance of peptidoglycan cross-links in bacteria cell wall?
- Cross-linkage is important because it is was pertains to the fluidity of the cell membrane. Without the cross linkage, it would just be layers of NAM and NAG, not able to be stretched or contracted when needed.
- without it, NAG and NAM are rigid structures
define quorum sensing
The process in which bacteria monitor their own population density or the presence of other species of bacteria by sensing the levels of signal molecules (e.g., N-acylhomoserine lactone) released by the microorganisms. When these signal molecules reach a threshold concentration, quorum-dependent genes are expressed.
list specific examples of AHL in cell-to-cell communication
AHL is a molecule produced by many Gram Negative organisms during quorum sensing; it induces the expression of virulence genes.
define biofilm
Organized microbial communities encased in extracellular polymeric substances and associated with surfaces, often with complex structural and functional characteristics.
how do microbes in biofilms interact with each other?
- Waste product of one may be the energy product of another
- Quorum sensing
what type of surface is more appropriate for biofilm formation?
- Can form on virtually any surface once it has been conditioned by proteins and other molecules present in the environment
- Water-air interfaces
How does biofilm formation interfere with antibiotic formation?
- Biofilm microbes release extracellular polymeric substances (EPS), which are not present in normal prokaryotic cells, so the antibiotics can’t attack. In addition, the EPS layers are too thick to attach to the microbes present on it
- In addition, persisters repopulate biofilm microbes once treatment has ended
What is a chemostat and how does it work?
- continuous culture apparatus that feeds medium into the culture vessel at the same rate as medium containing microorganisms is removed; the medium in a chemostat contains one essential nutrient in a limiting quantity
How do chemostats work?
- A chemostat maintains a stable chemical environment by continuously removing “old” medium and adding “fresh” medium.
what are the benefits of growing culture in a chemostat?
allows organisms to be grown under constant environmental conditions, at a steady state of growth . It also allows the experimenter to closely control environmental conditions and observe their impact on growth.
saturated vs unsaturated
- saturated: solid at RT, straight
- unsaturated: liquid at RT, bent
LPS and porin are only in gram negative and teichoic acid is only in gram positive
true
medium for cyanobacteria
1.5 g/L of NaNO3 .004 K2HPO4 X 3H2O .075 MgSO4 X 7H2O .036 CaCl2 x H2O .006 Ferric ammonium citrate .001 EDTA .02 Na2CO3 trace metal solution 1 ml/L final pH: 7.4
medium for e. coli
1.0 g/L glucose
16.4 NaHPO4
1.5 KH2PO4
2.0 (NH4)2SO4
.2 MgSO4 x 7H2O
.01 CaCl2
.0005 FeSO4 x 7 H2o
final pH: 6.8-7.0
gram positive and cocci disease
- staphylococci (clusters)
- streptococci (chains)
gram negative and cocci disease
- neisseria, causes gonorrhea. eye infections, STDs, and PID
gram positive and bacilli disease
clostridium and bacillus
gram negative and bacilli disease
salmonella and e. coli
vibrio disease
cholera, water borne disease
spirochete
lyme disease
