Final Exam: Topics 1 - 14 Flashcards
Define microbiology and microorganisms.
Microbiology: The study of living things too small to be seen with the untrained eye
Microorganisms: an organism of microscopic size
Use the appropriate units when using metric measurements for microorganisms.
Meter: 100 m, 1 m
Centimeter: 10-2 m, 0.01 m, 1/100 m hundreth of a meter
Millimeter: 10-3 m, 0.001 m, 1/1,000 m thousandth of a meter
Micrometer: 10-6 m, 0.000001 m, 1/1,000,000 m millionth of a meter
Nanometer: 10-9 m, 0.000000001 m, 1/1,000,000,000 m billionth of a meter
Angstrom: 10-10 m, 0.0000000001 m, 1/10,000,000,000 m
ten billionth of a meter
Picometer: 10-12 m, 0.000000000001 m, 1/1,000,000,000,000 m trillionth of a meter
Recognize the relative sizes of microbes.
about 1/10th the size of a typical human cell (7.5 um to 150 um)
Explain the properties of being unicellular vs multicellular and autotrophic vs heterotrophic.
Unicellular: a single cell; All prokaryotes are unicellular. Eukaryotes can be unicellular or multicellular
Multicellular: multiple cells that carry out different functions (cellular specialization)
Solve serial dilution problems to solve for OCD and calculate total dilution.
General dilution Equation: V1D1=V2D2
V1 = Volume of the first sample (or stock) added
V2 = Final volume in new tube (diluent + V1)
D1 = Dilution of first sample (=1 if stock–undiluted)
D2= Final dilution in a new tube
If D1=1 (the stock solution that is not diluted), then this is simplified to the Dilution Factor equation on the next slide.
Dilution factor: (Amount or volume original solution added)/ (total amount or volume made)
Example: You add 10 µL of stock to 990 µL of water.
What is the dilution within Tube 1?
D2 = (V1D1)/V = V1/V
D2= 10.0 macroliters/ 1000.0 macroliters = 1/100 = 10^-2
Original cellular density equation: OCD = CFU/(v x D)
CFU= # of colonies on the plate
v= volume plated
D= total dilution
Example: After making a series of dilutions of a bacterial culture and plating 0.1mL each dilution the plates are incubated, and colonies are counted. One plate has 40 colonies on it. The total dilution for that plate is 1/1000 = 0.001.
What is the OCD of the starting culture?
OCD= CFU/ (v x D)
CFU= # of colonies on the plate = 40 cfu
v= volume plated = 0.1mL
D= total dilution = 0.001
OCD = 40cfu/(0.1mL)(0.001) = 400,000 CFU/mL or 4 X 10^5 CFU/mL
Discuss the contributions of Van Leeuwenhoek, Redi, Spallanzani, Pasteur, Jenner, Semmelweis, Lister, Koch, Flemming, Hinton, Lederberg and Woese to the field of microbiology.
Van Leeuwenhoek: “Father of Microbiology”
Linen merchant who created high quality magnifying lenses that could magnify 500X
Discovered protozoa and named them “animalcules”
“In all falling rain, carried from gutters into water-butts, animalcules are to be found;…and that in all kinds of water, standing in the open air, animalcules can turn up. For these animalcules can be carried over the wind , along with the dust floating in the air.”
Antoine van Leeuwenhoek, 1702
Redi: Used controlled experiments to test whether maggots could spontaneously arise on meat.
Open jars: Maggots on meat
Closed (sealed) jars: No maggots on meat
Jars covered with fine mesh: No maggots on meat
Spallanzani: Used controlled experiments to test whether microbes arose from nutrient broth.
Nutrient broth (not heated): Microbe growth
Nutrient broth (heated): No microbe growth
Pasteur: Numerous contributions to the field including the process of fermentation, pasteurization, pure culture, the autoclave, and developed the rabies vaccine.
Also, did experiments to test spontaneous generation.
Used an S-shaped flask to test whether microbes are found in the air or generate spontaneously. Microbes are kept out, but air is let in.
Nutrient broth placed in S-flask, heated, not sealed: No microbe growth
Nutrient broth placed in S-flask, heated, then sealed, then neck broken off: Microbe growth
Jenner: developed the first vaccine to smallpox.
Demonstrated that inoculations of cow pox could prevent smallpox.
Semmelweis: Prior to the 1800, handwashing was not a routine practice in hospitals.
Found that washing hands with a chlorinated lime solution dramatically reduced rates of puerperal fever and death in patients.
Lister: introduced the principles of sterile surgery.
Revolutionized surgery in the 1800s.
Introduced carbolic acid (phenol) to sterilize instruments and clean wounds.
Koch: developed method to prove microorganism cause of disease.
His major contribution was the Germ Theory of Disease which he developed while studying Bacillus anthracis.
Flemming: Discovered naturally occurring antibiotics, including penicillin in 1928.
Discovered lysozyme in 1921.
Hinton: Developed widely used, highly accurate tests for syphilis
First black professor at Harvard
Lederberg: Considered the “Father of Microbial Genetics”
Discovered that bacteria can exchange genes by transfer of plasmids or by bacterial viruses (phage).
Woese: Pioneer in the field of molecular taxonomy.
Discovered the third domain of life (Archaea)
Revised the tree of life
Describe the first organisms on earth, their properties (cell type, metabolism) and how long ago they lived.
All life started from the same prokaryotic ancestor, but now there is vast diversity.
Archaea, bacteria, and Eucarya
1.3 million species named
Approximately 8.7 million species exist
Explain the Endosymbiotic theory of the evolution of mitochondria and chloroplasts.
Endosymbiotic theory is when the mitochondria and chloroplast in eukaryotic cells were once aerobic bacteria (prokaryote) that were ingested by a large anaerobic bacteria (prokaryote), which explains the origin of eukaryotic cells.
Mitochondria and chloroplasts likely evolved from engulfed prokaryotes that once lived as independent organisms. At some point, a eukaryotic cell engulfed an aerobic prokaryote, which then formed an endosymbiotic relationship with the host eukaryote, gradually developing into a mitochondrion.
Recognize how molecular phylogenetics led to a major change in how organisms are classified.
Each species retains some characteristics of its ancestor.
Grouping according to common properties implies that a group of organisms evolved from a common ancestor.
Morphology
Fossils
Molecular data (rRNA)
Compare and contrast three domains relation to their characteristics such as cell type, cell wall composition, plasma membrane composition, antibiotic sensitivity, and ribosome structure.
Bacteria: prokaryote, unicellular, hydrocarbon chains attached to glycerol by ester linkages, peptidoglycan, and is antibiotic sensitive.
Archaea: prokaryotic, unicellular, hydrocarbon chains are attached to glycerol by ether linkages, no peptidoglycan (usually S-layer), and not antibiotic sensitive.
Eukarya: Eukaryotic, multicellular, hydrocarbon chains attached to glycerol by ester linkages, no peptidoglycan (cellulose-plants chitin-fungi), and isn’t antibiotic sensitive. Each domain has a unique rRNA structure.
Relate how we define eukaryotic species, prokaryotic species, and virus species.
Prokaryotic species: A group of prokaryotes that have similar characteristics: appearance, physiology, and genes.
Definitions:
Culture: bacteria grown together in laboratory media
Clone: Population of cells derived from a single cell
Strain: Genetically different cells that have been derived from a clone
Eukaryotic
A cell characterized by the presence of a nucleus and other membrane-bound organelles. Eukaryotes can be unicellular (protists) or multicellular (fungi, plants and animals).
Prokaryotic
An organism whose cells do not have an enclosed nucleus, such as bacteria.
viral species
a group of viruses sharing the same genetic information and ecological niche (host)
the two kingdoms Carolus Linnaeus began taxonomy with
Plantat and Animals
Explain the difference between classification and identification, and why classifying microorganisms is difficult.
Classification: Placing organisms in groups of related species. Lists of characteristics of known organisms.
Identification: Matching characteristics of an “unknown” organism to lists of known organisms.
Clinical lab identification
The species of bacteria are not stable. They regularly try to adopt into changed environment by changing their genetic material. So, it is not possible to easily and stable classification of the bacteria at the species level.
Explain the difference characteristics used to classify bacteria: morphology (shapes and grouping), gram stain (positive vs negative), motility, nutrient requirements (different groups based on oxygen use), antibiotic resistance, and genetics and metagenetics (GC content and 16s rRNA sequencing).
Morphology
Coccus: round
Bacillus: rod
Vibrio: curved rod
Coccobacillus: short rod
Spirillum: spiral
Spirochete: long, loose spiral
The ability to move is often accomplished through the presence of flagella, tail like appendages
Obligate aerobes (1)
MUST have oxygen to survive
Facultative anaerobes (3)
Can use oxygen if it is there but can also live without
Microaerophiles (4)
Require a low concentration of oxygen
Obligate anaerobes (2)
Prefer to grow without oxygen
May be harmed by oxygen
Aerotolerant anaerobes (5)
Do not use oxygen but can tolerate it
Antibiotic Resistance: Due to the presence of antibiotics in the environment, some strains have become resistant.
Acquire plasmids carrying antibiotic resistance genes by horizontal gene transfer.
Genomics is the analysis of the complete DNA sequence of an organism.
Gene content and organization
G+C content
DNA-DNA hybridization
Average nucleotide identity (ANI)
DNA extraction and analysis from microbial communities= Metagenomics
Determined 3 domains based on 16s rRNA sequence:
Bacteria
Archaea
Eukarya
Domain is a distinction above kingdom.
Describe the ways we identify bacterial species.
Biochemical tests: Presence of bacterial enzymes and Morphological characteristics: Shape/arrangement of cells, cell structures (more useful for eukaryotic microbes)
Know the different morphologies and arrangements of prokaryotic cells
Prokaryotic Cell Morphology(shapes) and Arrangement (groups or single cells):
Morphology
Coccus: round
Bacillus: rod
Vibrio: curved rod
Coccobacillus: short rod
Spirillum: spiral
Spirochete: long, loose spiral
Arrangement:
Coccus(plural: cocci): single coccus
Diplococcus(plural: diplococci): pair of 2 cocci
Tetrad(plural: tetrads): grouping of 4 cells arranged in a square
Streptococcus(plural: streptococci): chain of cocci
Staphylococcus(plural: staphylococci): cluster of cocci
Bacillus(plural: bacilli): single rod
Streptobacillus(plural: streptobacilli): chain of rods
Understand the difference between selective and differential media.
Selective media is used to inhibit growth of some organisms, while encourage growth of others
Differential media is used to differentiate closely related or groups of organisms.
Describe how biochemical tests can be used to identify bacteria.
Mannitol salt agar (MSA)
High salt in media inhibits growth of most bacteria but selects for Staphylococcus species.
Differentiates S. aureus from other species based on their ability to ferment mannitol
Enzyme tests: presence of certain enzymes can be used to identify bacteria.
Examples:
Indole test
Urea broth
Indole test: Hydrolysis of tryptophan by tryptophanase to pyruvate + ammonia + indole
Urea broth: tests for production of the enzyme urease.
Urease breaks down urea.
Urea is a break down product of certain amino acids that is excreted in the waste of many animals.
Urea can provide organisms with a source of nitrogen in the form of ammonia (NH3).
Metabolic tests: tests for presence of a certain metabolic pathway.
Examples:
Phenol red broth: tests for fermentation of carbohydrates.
Different carbohydrates can be tested.
Tests for production of acidic fermentation products and gas.
Phenol red broth results:
Yellow: fermentation
Red/pink: no fermentation
Understand why dichotomous keys are used in bacterial identification and how to interpret one.
Key for identification of organisms based on a series of choices between alternative characteristics.
First characteristic should distinguish between broad categories (such as cell morphology or Gram stain)
Subsequent characteristics should an organism or separate other organisms.
Describe the properties of electromagnetic waves: wavelength, amplitude, and frequency.
Wavelength: distance from one peak to the next
Amplitude: the height of each peak
Frequency: number of wavelengths/ unit time
Describe the following properties of light: reflection, absorbance, transmission, interference, diffraction, refraction, and refraction index.
Reflection: when light bounces off a material
Absorbance: when a material catches the energy of a light wave
Transmission: when the light wave travels through a material
Opaque vs Transparent
Interference: when light waves interact with each other to make complex motion patterns (like two pebbles thrown in a lake)
Diffraction: when light bends or scatters in response to interacting with small openings or objects.
Refraction: when light waves change direction upon entering a medium
Refractive index: The degree to which a material slows transmission speed.
Explain the concepts of magnification, resolution, and contrast as they relate to microscopy.
Magnification is an increase in size.
Resolution is the ability to see two different points as separate. Determined by:
wavelength (shorter= higher resolution)
numerical aperture (NA): the ability of a lens to gather light (the higher the aperture the higher the resolution)
Contrast is differences is light intensity
How we see things
Most biological material is water
Contrast between the specimen and the background is critical
Different forms of microscopy we will cover:
Light Microscopy
Brightfield
Darkfield
Phase-Contrast
Differential Interference Contrast (DIC)
Fluorescence Microscopy
Confocal Microscopy
Electron Microscopy
Transmission Electron Microscope (TEM)
Scanning Electron Microscope (SEM)
Explain the difference between a simple microscope and a compound microscope.
Simple: a microscope in which the light only passes through one lens. (van Leeuwenhoek)
Compound: a microscope in which the light passes through two lenses (Galileo)
Understand the principles and limitations of light microscopy.
Principles:
The light microscope is an instrument for visualizing fine detail of an object. It does this by creating a magnified image through the use of a series of glass lenses, which first focus a beam of light onto or through an object, and convex objective lenses to enlarge the image formed.
Limitations:
light microscope cannot be small than the half of the wavelength of the visible light, which is 0.4-0.7 µm. When we can see green light (0.5 µm), the objects which are, at most, about 0.2 µm.
Discuss special types of light microscopy: brightfield, darkfield, phase-contrast, DIC, fluorescence (including immunofluorescence), and confocal
brightfield: Produces a dark image on a bright background
Can be monocular or binocular
Compound microscopes have two different kinds of lenses
Ocular lens
Objective lens
Need to calculate TOTAL magnification
dark field: Like brightfield with a modified condenser (opaque light stop)
Oblique light reflects off the edges of the specimen
Often better resolution than brightfield
Darkfield allows high contrast, high resolution images without stain.
phase-contrast: Uses refraction and interference to create high-contrast, high resolution images of live samples.
DIC: Differential Interference Contrast Microscopy (Nomarski)
Uses interference patterns to enhance contrast
Live specimens appear 3D.
Can view structures inside cells.
fluorescence: uses fluorescent chromophores. Fluorescent chromophores absorb light (excitation is usually UV) and then emit it as visible light.
Can be natural (chlorophyll) or a stain
Examples: Texas Red and FITC
Creates high resolution images on a dark background
Can do multiple staining at one time
UV is a hazard and can be expensive
Immunofluorescence uses antibodies to visualize specific proteins.
Antibodies are protein molecules produced by the immune system that attach to specific pathogens to kill or inhibit them.
A chromophore can be attached to the antibody to detect the protein in a specimen
Confocal Microscopy takes images at many different z planes, then a computer constructs it into a 3D image.
Fluorescence dyes are often used in conjunction with this technology to increase contrast and resolution.
Useful for resolving all parts of thick samples that can be examined alive
Very complex and expensive instrument
Compare and contrast of transmission and scanning electron microscopy, and atomic force microscopy.
Electron microscopy: Light microscope are limited by the wavelengths of visible light (up 1500X)
Electrons can act like waves with a very short wavelength, so get amazing resolution and can magnify 100000x.
The specimen must be prepared so cannot be alive.
Two main types:
Transmission Electron Microscope
Scanning Electron Microscope
Transmission Electron Microscope: Uses a beam of electrons focused by magnets
Beam passes through a sample and then runs into the detector the captures the image.
Specimens are a very thin section (20-100nm thick)
Good for internal structures
Scanning Electron Microscopy: Creates an image by collecting electron that are knocked off off a specimen with a beam of electrons
Specimens are dried and often coated with gold
Good for looking at the surfaces of larger objects or smaller samples
Atomic force microscopy: can be used in several ways, including using a laser focused on a cantilever to measure the bending of the tip of a probe passed above the specimen while the height needed to maintain a constant current is measure; useful to observe specimens at the the atomic level and can be more easily used with nonconducting samples.
Explain the different between direct and indirect counts of bacteria. You should also be able to explain all the following methods: direct microscopic count, Coulter counter, serial dilution followed by a plate count, the Most Probable Number, and spectrophotometry.
Direct counting methods count the number of organisms present in a sample.
1. Direct microscopic counts using a Petroff-Hauser chamber.
- Take a small known volume of a culture to a calibrated slide and count the number of cells under a light microscope.
- One disadvantage of this method is that you are counting dead cells too, but you can use a secondary stain to fix this.
2. Coulter Counter
- The Coulter Counter counts the changes in electrical resistance in a saline solution.
- Each bacterium causes a change in resistance and is counted.
3. Serial dilution, followed by plate count
- Serial dilution is a method for determining the number of living bacterial cells in a culture by making a series of dilutions and plating the diluted cultures on agar plates.
- Plate Counts: spread a small amount of culture on a bacterial plate and wait for colonies to grow.
-Counts viable cells
> Problem: only plates with 30-300 colonies are countable
> To do this: you would have to spread 0.0000001 mL (0.1 μl) on a plate… not possible…
> SOLUTION? Serial Dilution
> Systematically reduces the concentration of cells in a sample, so you can get plate a volume that will yield 30-300 colonies on a plate.
4. Most probable number
- The Most Probable Number method is used when bacterial count is too low for other methods.
- Evaluates detectable growth by observing changes in turbidity or color due to metabolic activity.
- Serial dilution in MEDIA to see when culture is diluted out.
- Use MPN table for final determination of titer
Indirect counting measure the turbidity (how cloudy) the sample is and is used as as estimation or to compare cultures.
Be able to solve serial dilution problems including calculating the OCD of a culture.
General dilution Equation: V1D1=V2D2
V1 = Volume of first sample (or stock) added
V2 = Final volume in new tube (diluent + V1)
D1 = Dilution of first sample (=1 if stock–undiluted)
D2= Final dilution in new tube
If D1=1 (stock solution that is not diluted), then this is simplified to the Dilution Factor equation on the next slide.
Dilution factor: (Amount or volume original solution added)/ (total amount or volume made)
Example: You add 10 µL of a stock to 990 µL of water.
What is the dilution within Tube 1?
D2 = (V1D1)/V = V1/V
D2= 10.0 macroliters/ 1000.0 macroliters = 1/100 = 10^-2
Original cellular density equation: OCD = CFU/(v x D)
CFU= # of colonies on the plate
v= volume plated
D= total dilution
Example: After making a series of dilutions of a bacterial culture and plating 0.1mL each dilution the plates are incubated, and colonies are counted. One plate has 40 colonies on it. The total dilution for that plate is 1/1000 = 0.001.
What is the OCD of the starting culture?
OCD= CFU/ (v x D)
CFU= # of colonies on the plate = 40 cfu
v= volume plated = 0.1mL
D= total dilution = 0.001
OCD = 40cfu/(0.1mL)(0.001) = 400,000 CFU/mL or 4 X 10^5 CFU/mL
Compare and contrast prokaryotic DNA and location from eukaryotic DNA and location.
The prokaryotic genome is different than the eukaryotic genome.
Prokaryotic genomes are smaller (1/1000 of the human genome) and usually circular.
They are haploid, meaning they only have one copy of every gene.
Prokaryotes often have additional DNA called plasmids, small circular pieces of DNA with non-essential genes.
They are found in the nucleoid and associate with nucleoid-associated proteins that package and organize the DNA.
Eukaryotic cells keep their chromosomes in the nucleus
Have multiple, linear chromosomes
Can be haploid or diploid
DNA is packaged with proteins called histones (also for Archaea).
Know how prokaryotes and eukaryotes divide.
Prokaryotes divide by binary fission and must replicate their DNA.
Bacteria reproduce by BINARY FISSION
The bacteria chromosome is duplicated (DNA replication)
One copy goes to each daughter.
Differentiate horizontal and vertical gene transfer.
horizontal gene transfer: when bacterial genetic recombination occurs
Vertical gene transfer is the transfer of genetic information, including any genetic mutations, from a parent to its offspring.
Identify and be able to describe the parts of the cell making up the cell envelope: cell membrane, cell wall, and glycocalyx.
The cell envelope encloses the cytoplasm and internal structures.
Comprised of up to three layers
Cell membrane (inner most)
Cell wall (middle)
Glycocalyx (outer most)
All cells have a plasma membrane which is semi-permeable.
Composed primarily of a bilayer of amphipathic phospholipids, but also has proteins embedded
Structure is described by using the fluid mosaic model.
Describe how molecules move across the plasma membrane by diffusion, osmosis, facilitated diffusion, and active transport.
Diffusion is the tendency of molecule to move from an area of high concentration to low.
Osmosis is diffusion of water.
Water will move from areas of higher water concentration to areas of lower water concentration. This inversely corresponds to the solute concentration. Water moves across the membrane to help ‘dilute’ the solute until there is an equivalent % of water to solute on each side.
Facilitated Diffusion: protein helps large, polar and/or charge molecules move WITH their concentration gradient.
Active Transport: protein helps large, polar and/or charge molecules travel AGAINST their concentration gradient. Requires energy (ATP or concentration gradient).
Define the terms hypertonic, hypotonic, and isotonic and be able to predict which way water will flow.
Hypertonic:
Solution with the higher solute concentration
Pulls water towards it (greater pulling power)
Hypotonic:
Solution with lower solute concentration
Water is pulled from it (lower pulling power)
Isotonic:
Same pulling power for water on both sides of membrane
Flow of water is equal in both directions, so the net flow is zero.
Compare and contrast the Gram positive and Gram-negative cell walls and eukaryotic cell walls.
Gram positive (thick layer of peptidoglycan)
Gram positive bind stain better because they have a thick layer of peptidoglycan.
Stain Purple
Gram-positive bacteria have a very thick cell wall that often contains teichoic acid.
Gram negative (thin layer of peptidoglycan)
Gram negative bacteria only have a little peptidoglycan, so don’t hold on to the stain.
Stain Pink
Gram-negative bacteria have a thin layer of peptidoglycan and an inner membrane (IM) and an outer membrane (OM) separated by the periplasmic space.
Recognize and describe the function of inclusion bodies, ribosomes, and thylakoids.
Inclusion bodies:
- Inclusions allow prokaryotes to store excess nutrients or other materials.
- Not membrane bound
Usually store nutrients
> Glycogen or starch for carbon stores
> Polyphosphate granules for inorganic phosphate used in metabolism
> Sulfur granules for metabolism in Thiobacilius
- Sometimes can store other things like gas or magnetic iron.
Ribosomes:
- All cells have ribosomes, but the prokaryotic ribosome is a bit different.
- Ribosomes are the protein synthesis machinery made of a mix of RNA and proteins.
- Prokaryotic ribosomes are smaller (70s) than eukaryotic ones (80s).
- Many antibiotics target the prokaryotic ribosome.
Thylakoids:
- The principal functions of thylakoids are the trapping of light energy and the transduction of this energy into the chemical energy forms, ATP and NADPH. During this process, water is oxidized and oxygen is released.
Describe how endospores are formed and describe the life cycle from vegetative state to endospore, etc.
Bacterial cells are generally vegetative, undergoing cell division and metabolism, but some can form endospores.
Dormant bodies that are resistant to heat, radiation, and chemicals, freezing, dehydration
Metabolically active vegetative cells can undergo sporulation in response to external stimuli
Found among the Gram positive Bacillales and Clostridiales.
Most well-known genera are Bacillus and Clostridium
Endospores are desiccated and extremely hard to kill.
Consist of several layers and many of the same structures found in vegetative cells
Contain very little water
Can persist in the environment for long periods of time
Identify the prokaryotic flagellum and recognize the mechanism involved in motility.
Prokaryotic flagellum is a rigid spiral made of flagellin protein and spins 360 degrees. This is different from eukaryotic flagella that move only 180 degrees, like a whip, is flexible, and made of microtubules.
Motility is movement towards or away from stimuli.
Flagella allow bacteria to move in response to chemical signals (chemotaxis), light (phototaxis), or changes in temperature (thermotaxis)
Compare and contrast the cell membrane and cell wall composition and structure of bacteria, archaea, and eukaryotes
Cells walls in Archaea and Eukarya are quite different than in Bacteria.
Archaeal cell walls are not made of peptidoglycan
Usually, pseudopeptidoglycan where NAM subunit is replaced with something else
Could be made of another glycoprotein or polysaccharide
Eukarya cell walls are either made of cellulose (plants) or chitin (fungi)
Compare and contrast positive and negative chemotaxis.
> Positive –taxis: Movement towards a stimulus
Negative –taxis: Movement away from a harmful stimulus
Identify the function of the fimbriae and pili.
Fimbriae and pili – allow for specialized attachments
Fimbriae and pili are structurally similar but have some key differences.
Fimbriae
- Shorter and more numerous, covering the entire surface of the cell
- Used to adhere to surfaces or other cells.
- Can be a pathogenetic determinant.
Pili
- Longer and less numerous
- Involved in conjugation.
Compare and contrast anabolic and catabolic reactions.
Anabolic reactions involve the building of larger, complex molecules from smaller, simpler ones, and require an input of energy. (requires energy, builds larger, complex molecules from smaller, simpler ones and forms chemical bonds between molecules)
Catabolic reactions are the opposite of anabolic reactions, and break the chemical bonds in larger, more complex molecules. (releases energy, breaks down large, complex molecules into smaller, simpler ones and breaks chemical bonds within molecules)
Describe the two ways energy harvested from catabolic reactions can be stored. Know the oxidized and reduced forms of NAD+/NADH and FAD/FADH2 and where the energy is store in the ATP molecule.
Molecular energy stored in the bonds of complex molecules is released in catabolic pathways and harvested in such a way that it can be used to produce high-energy molecules, which are used to drive anabolic pathways.
NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule.
The oxidized form of flavin adenine dinucleotide is FAD, and its reduced form is FADH2.
A living cell must be able to handle the energy released during catabolism in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell.
This chemical energy is stored in the pyrophosphate bond, which lies between the last two phosphate groups of ATP.
Be able to explain the following enzyme related terms: enzyme, substrate, active site, allosteric site.
Enzymes: major cellular catalysts
typically proteins (some R N A s)
highly specific as a result of structure
substrate: in reaction, enzyme combines with reactant (substrate: chemical reactants of an enzymatic reaction), forming enzyme-substrate complex, releasing product and enzyme
active site: region of enzyme that binds substrate
an allosteric site, a location other than the active site, and still manages to block substrate binding to the active site by inducing a conformational change that reduces the affinity of the enzyme for its substrate.
allosteric site: location within an enzyme, other than the active site, to which molecules can bind, regulating enzyme activity
Compare and contrast autotroph vs. heterotroph and phototroph vs. chemotrophs.
Autotrophs convert inorganic CO2 to organic compounds.
Heterotrophs get their carbon from complex organic compounds (often from autotrophs)
Phototrophs get their energy from electron transfer from light.
Chemotrophs get their energy from electrons by breaking chemical bonds
Identify the two different types of ATP production.
A T P generated through 1 of 3 mechanisms
Substrate-level phosphorylation: energy-rich substrate bond hydrolyzed directly to drive A T P formation (e.g., hydrolysis of phosphoenolpyruvate)
Oxidative phosphorylation: Movement of electrons generates proton motive force (electrochemical gradient) used to synthesize A T P
Photophosphorylation: light used to form proton motive force
Compare and contrast aerobic respiration, anaerobic respiration, and fermentation.
Respiration:
Aerobic respiration:
Terminal acceptor is oxygen
Anaerobic respiration:
Alternative terminal electron acceptors
NO3-, SO4-2, CO2
Lower energy yields than O2
Fermentation (anaerobic):
Organic substrate for NADH oxidation
Low energy yield
Know the 4 phases of respiration, what goes in, what comes out, where it occurs, and if oxygen is requires.
Four Phases:
Glycolysis: Energy is added to a glucose molecule by adding a phosphate group to each end.
Carbon-carbon bond is broken, 2 NAD+ are reduced, and 2 inorganic phosphates are added.
Phosphates are transferred from carbon to ADP to form ATP (staring material: glucose, products: 2 NADH, 2 ATP(net), and 2 pyruvate, this takes place in cytoplasm and no oxygen is required)
Transition reaction:
Starting materials: 2 pyruvate
Products:
2 NADH
2 CO2
2 acetyl CoA
Takes place in: Mitochondrial matrix
Oxygen required? YES
Krebs cycle (also known as Citric acid cycle or TCA cycle): Krebs Cycle
Starting materials: 2 acetyl CoA
Products:
4 CO2
6 NADH
2 FADH2
2 ATP
Takes place in: mitochondria
Oxygen required? YES
Electron transport chain:
Starting materials: NADH, FADH2, O2
Products: ATP:
3 from each NADH
2 from each FADH2
H2O
Takes place in: mitochondria
Oxygen required: yes
Understand the reasons organisms might use fermentation instead of respiration.
When certain organisms can’t do cellular respiration, they do glycolysis, followed by fermentation instead.
Many cells are unable to carry out respiration because of one or more of the following circumstances:
Lacking enough of any appropriate, inorganic, final electron acceptor to carry out cellular respiration. (TEMPORARY)
Lacking genes to make appropriate complexes and electron carriers in the electron transport system. (PERMENANT)
Lacking genes to make one or more enzymes in the Krebs cycle. (PERMENANT)
Be able to explain the 2 phases of photosynthesis, their reactants, products, and major steps.
Light-dependent reactions:
Energy from sunlight is captured by photopigments and stored as chemical energy.
The light-dependent reactions produce ATP and either NADPH or NADH to temporarily store energy. These energy carriers are used in the light-independent reactions to drive the energetically unfavorable process of “fixing” inorganic CO2 in an organic form, sugar.
Light-independent reactions:
Chemical energy from the light-dependent reaction is used to build sugar molecules from CO2
The light-independent reactions (Calvin cycle) use the chemical energy from the light-independent reactions and uses it to build CO2 into sugar.
CO2+H2O –> C6H12O6+O2
Know the difference between oxygenic and anoxygenic photosynthesis.
Oxygenic:
Water is source of e- and H+
O2 is released
Anoxygenic:
Compounds other than water are the electron and proton donor
Purple non-sulfur bacteria use dissolved organic material like succinate or malate or hydrogen gas
(1. Sunlight/energy
2. Light-dependent reactions
3. Light-independent reactions)
Know how microbes grow in number by binary fission, including the step of binary fission.
Binary fission is the process of bacterial cell division.
Each bacterial cell makes an exact copy of itself.
The time required to perform a division is the generation time.
Wide diversity in Generation time
Ranges from 20 minutes in a well fed and aerated E. coli culture to weeks in a Mycobacterium sp culture to centuries in some oligotrophic environments
Binary Fission Steps
1. DNA replication
2. Cell elongation
3. Formation of division septum
4. Cell separation
Describe the 4 different phases of microbial growth and what the cells are doing at each phase and why.
- Lag: No division
Cells are settling into their new environment
Lots of metabolic activity as cells get ready to divide
- Log: Once cells have enough energy and materials they start rapidly dividing
Growth is logarithmic
The relationship between time and number of cells is not linear but exponential.
- Stationary: Growth slows and population size reaches equilibrium
of cells made = # of cells dying
Growth rate is 0
- Death/decline: More cells die than are being made
Cells are killed by built up waste products or lack of nutrients
Describe the different physical and chemical growth requirements of bacteria.
Physical requirements for growth: temperature, pH, and osmotic pressure/salt concentration
Chemical growth requirements:
6 most common elements in organisms?
C,H,O,N,P,S
Other common elements:
K, Mg, Fe, Ca, Mn
Trace Elements
Zn, Co, Cu, Mo
Name and describe the different categories of bacteria in respect to temperature preference (psychrophiles, mesophiles, thermophiles, and hyperthermophiles) and pH preference (acidophiles, neutrophiles, and alkaliphiles).
Temperature preference;
Psychrophiles: also known as psychrotolerant, prefer cooler environments, from a high temperature of 25 °C to refrigeration temperature about 4 °C. They are found in many natural environments in temperate climates.
Mesopholes: adapted to moderate temperatures, with optimal growth temperatures ranging from room temperature (about 20 °C) to about 45 °C. As would be expected from the core temperature of the human body, 37 °C (98.6 °F), normal human microbiota and pathogens (e.g., E. coli, Salmonella spp., and Lactobacillus spp.) are mesophiles.
Thermophiles: Organisms that grow at optimum temperatures of 50 °C to a maximum of 80 °C
Hyperthermophiles: characterized by growth ranges from 80 °C to a maximum of 110 °C, with some extreme examples that survive temperatures above 121 °C, the average temperature of an autoclave.
pH preference;
acidophiles: Microorganisms that grow optimally at pH less than 5.55
neutrophiles: meaning they grow optimally at a pH within one or two pH units of the neutral pH of 7
alkaliphiles: microorganisms that grow best at pH between 8.0 and 10.5. Vibrio cholerae, the pathogenic agent of cholera, grows best at the slightly basic pH of 8.0; it can survive pH values of 11.0 but is inactivated by the acid of the stomach.
Explain how bacteria are adapted to deal with osmotic pressure and high salt environments.
Growth is highest at the OPTIMAL GROWTH TEMPERATURE.
The lowest temperature the bacteria can survive and reproduce is called its minimum growth temperature.
The highest the bacteria can survive and reproduce is called its maximum growth temperature.
Higher up on the extreme temperature scale we find the hyperthermophiles, which are characterized by growth ranges from 80 °C to a maximum of 110 °C, with some extreme examples that survive temperatures above 121 °C, the average temperature of an autoclave.
Not much protection is available against high osmotic pressure. In this case, water, following its concentration gradient, flows out of the cell. This results in plasmolysis (the shrinking of the protoplasm away from the intact cell wall) and cell death. This fact explains why brines and layering meat and fish in salt are time-honored methods of preserving food.
Microorganisms called halophiles (“salt loving”) actually require high salt concentrations for growth. These organisms are found in marine environments where salt concentrations hover at 3.5%.
Be able to explain the different kinds of bacteria in respect to oxygen usage (obligate aerobes, facultative anaerobes, microaerophile, obligate anaerobes) and how thioglycolate tubes are used to test this.
Obligate aerobes: need abundant oxygen.
Facultative anaerobes: thrive on O2 but can live for a while without it
Obligate anaerobes: oxygen is toxic to them
Aerotolerant anaerobes: do not use oxygen but can tolerate it
Microaerophiles: require a small amount of oxygen
We can test the oxygen preference of a species by growing bacteria in thioglycolate tubes.
Explain the difference between agar cultures vs broth, general vs specialized medium, chemically defined vs complex media, selective vs differential media
Bacteria can be grown on solidified agar medium either in a test tube (slant) or in a petri dish.
You can also grow your microbe in a watery nutrient broth.
general, all-purpose and support many different organism
specialized: Enriched media for fastidious bacteria, with complex nutritional needs
chemically defined, meaning that every component is known and quantified. (Water, Glucose, NH4Cl, KH2PO4, K2HPO4, MgSO4, Na acetate, Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glycine, Histidine, Isoleucine, Etc.)
complex, made of extracts or digests from yeast, meat, or plants so the components are undetermined and variable (Water, Peptone, Beef extract, NaCl)
Selective media inhibits the growth of unwanted microorganisms and supports the growth of the organism of interest by supplying nutrients and reducing competition
Differential media: make it easy to distinguish colonies of different bacteria by a change in the color of the colonies or the color of the medium.
Describe how we obtain a pure culture via plate streaking.
Obtaining a pure culture of bacteria is usually accomplished by spreading bacteria on the surface of a solid medium so that a single cell occupies an isolated portion of the agar surface. This single cell will go through repeated multiplication to produce a visible colony of similar cells, or clones.
Explain the term biofilm.
biofilm: complex ecosystem of bacteria embedded in a matrix
Define the terms genetics, genome, chromosome, gene, genetic code, genotype and phenotype.
Genetics: the study of how genes and how traits are passed down from one generation to the next.
genome: entire genetic content of a cell
chromosome: discrete DNA structure within a cell that controls cellular activities
gene: a sequence of DNA that codes for a single protein = one gene one polypeptide
genetic code: correspondence between mRNA nucleotide codons and the translated amino acids
Genotype: precise sequence of nucleotides found in that individual organism
For example: the sequence of the gene encoding the lactase enzyme
Phenotype: observable characteristics that result from the organism’s genotype
For example: ability to digest lactose
Explain DNA replication, including all the enzymes involved.
DNA replication is the process by which the genome’s DNA is copied in cells.
DNA replication is semi-conservative.
Semi-conservative means that each daughter strand has one parental strand and one newly synthesized strand.
The old strand is used as a pattern to make the new strand using complementary binding.
Step 1: Helicase breaks the hydrogen bonds holding the two strands together, so they separate
Step 2: DNA polymerase adds nucleotides to the growing new strand, complementing the bases on the template strand
Explain what is meant by the concept of The Central Dogma of Biology. Also, know
what is meant by “one gene – one polypeptide hypothesis.”
The Central Dogma of Biology describes the flow of information in the cell.
central dogma states that DNA organized into genes specifies the sequences of messenger RNA (mRNA), which, in turn, specifies the amino acid sequence of proteins.
a single protein = one gene one polypeptide
List the similarities and differences between DNA and RNA.
Both DNA and RNA are nucleic acids made of nucleotides involved in gene expression.
What are the differences between DNA and RNA?
bases (RNA: uracil, DNA: thymine)
Sugar (RNA: ribose, DNA: deoxyribose)
# of strands (RNA: 1, DNA: 2)
Describe process of transcription, indicate where and how transcription occurs in eukaryotic cells and where/how it occurs in prokaryotic cells. Be able to describe the enzyme involved, how it knows where to begin transcription, how it knows how to end transcription.
Translation is the decoding of the mRNA message into a polypeptide by the ribosome.
The language is called the GENETIC CODE.
Translation is the process of decoding the mRNA into a sequence of amino acids.
What is required for translation?
mRNA template
Ribosome: made of a mix of rRNAs and protein
tRNA
Transcription begins when RNA polymerase binds to a promoter sequence near the beginning of a gene (directly or through helper proteins).
RNA polymerase uses one of the DNA strands (the template strand) as a template to make a new, complementary RNA molecule.
Transcription ends in a process called termination. Termination depends on sequences in the RNA, which signal that the transcript is finished.
Eukaryotic transcription is carried out in the nucleus of the cell by one of three RNA polymerases, depending on the RNA being transcribed, and proceeds in three sequential stages: Initiation. Elongation. Termination.
Prokaryotic transcription is the process in which messenger RNA transcripts of genetic material in prokaryotes are produced, to be translated for the production of proteins. Prokaryotic transcription occurs in the cytoplasm alongside translation. Prokaryotic transcription and translation can occur simultaneously.
