Micro Lecture Questions

What are Koch's postulates?

1. The same pathogen must be present in every case of the disease. 2. The pathogen must be isolated from the diseased host and grown in pure culture. 3. The pathogen from the pure culture must cause the disease when it is inoculated into a healthy, susceptible laboratory animal. 4. The pathogen must be isolated from the inoculated animal and must be shown to be the original organism.

What is the resolution of the human retina? How does this compare to the size of a typical bacterial/archaeal cell?

150 micrometers vs .2 micrometers

What type of light interaction is involved in all these techniques?

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What technique led to the discovery of viruses?

A filtering technique

What is horizontal gene transfer and how has it changed our view of the tree of life?

A genetic exchange mechanism. Some genetic material can be passed from one microbe to another in the same generation instead of linearly from one generation to the next.

what is a microbe

A living organism that required a microscope to be seen by the human eye

What type (shape) of lens is used in light microscopy?

A single convex lense (parabolic).

How is ATP synthesized and what are examples of high energy phosphate-containing Molecules?

ADP to ATP via h+ gradient. 3 protons per atp.

What is the energy source for ABC transporters?

ATPase activity

What are advantages and disadvantages of using a wet mount?

Advantage: You can observe living cells in a natural state. For example, it's possible to see motility. • Disadvantage: Most cells are transparent so there's very little contrast making it hard to achieve high resolution. Sample may dry out quickly

What are the stages of the biofilm formation? What role do quorum sensing molecules play in this process?

Attachment, colonization, development, disperal.

How might heterotrophs and autotrophs cooperate in processing carbon in the Environment?

Autotrophs fix co2 and hetero just use them directly.

What are the three domains and which domains do microbes occur?

Bacteria, Archaea, Eukarya, and Microbes occur in all three

Why are special preparation methods needed to visualize cells using electron microscopy?

Because most biological materials lack sufficient density to scatter electrons and require chemical treatment to increase the contrast

Why is dark field microscopy useful for visualizing flagella?

Because the bacteria are not dead so the flagella are still moving and in general it is useful for seeing small structures.

What advantages might cells in a biofilm have over their planktonic counterparts?

Better protection due to close contact.

What features of a specimen can be visualized using confocal microscopy?

Biofilm and 3d reconstruction

What are examples of development programs in bacterial cells?

Biofilm, endosporms, exococys.

What lipids and proteins are specific to the gram negative outer membrane?

Braun/Murein lipoprotein and lipopolysacchardide.

What are examples of microbial or viral diseases that have affected large populations? Of these, which remain problematic?

Bubonic plague, TB, small pox, and AIDS TB and AIDS

How do slime layer and capsule differ?

Capsule: firmly attached and neatly organized Capsules prevent phagocytosis Slime layer: unorganized and loose; easily removed

Given an example of how microbes contribute to the biogeochemical cycling of essential elements?

Carbon cycle: cyanobacteria fix carbon dioxide into usable organic forms via photosynthesis Nitrogen cycle: Bacteria that contain the enzyme nitrogenase combine N2 with hydrogen to produce a useful form of nitrogen (such as ammonia)

What are persisters and why are they important in human health and disease?

Cells are called persister cells long-term survival increased virulence

What are the two alternative hypotheses for the cellular response in the death phase?

Cells are viable but not culturable and programmed cell death.

What are common approaches for labeling parts of a cell in fluorescence microscopy?

Chemical affinity: acridine binds to DNA and RNA Labeled antibodies: Antibodies to a specific protein linked to a fluorophore (immunofluorescence) Gene fusion: Some protein generate fluorescence, such as the green fluorescence protein (GFP). Protein fusions with GFP can be introduce into a cell and the partner protein can be visualized indirectly. DNA hybridization: DNA molecules carrying a fluorescence-labeled tag can be used to bind specifically, through base pairing, to complementary molecules in the cell

What specialized structures aid phototrophic cell in acquiring light for growth?

Chromatophores, thylakoids, chlorosomes, carboxysomes, gas vesicles, storage granules, nanotubes, anammoxosome.

How could you infer HGT of a gene?

Compare evolutionary history of that protein to history of other proteins in that organism.

What is the general structure of lipopolysaccharide? What functions are associated with LPS?

Consists of three parts • O side chain (O antigen) • core polysaccharide • lipid A. Importance • contributes to negative charge on cell surface • helps stabilize outer membrane structure • may contribute to attachment to surfaces and biofilm formation • creates a permeability barrier • protection from host defenses (O antigen) • can act as an endotoxin (lipid A)

How did Koch postulates further our understanding of disease mechanisms?

Criteria for establishing a causative link between an infectious agent and a disease

What physical characteristic of the object is exploited in phase contrast microscopy?

Cytoplasm and sub-cellular organelles

What is the difference between detection and resolution?

Detection is the ability to view the object, a resolution is the smallest distance by which two objects can be separated.

What distinguishes a eukaryote from a prokaryote? Why is this a poor definition?

Eukaryotes have their genetic material stored in a nucleus, whereas prokaryotes do not. There are exceptions to the definition from both Eukaryotes and Prokaryotes and some prokaryotes can be compartmentalization (like the article we read)

Where might these proteins be located in a gram negative organisms?

External to the cytoplasmic space.

How does simple diffusion differ from facilitated diffusion?

Facilitated diffusion helps solutes move across a membrane from a region of high concentration to one of lower concentration. It does not use energy and cannot move a molecule against its gradient. Coupled transport systems are those in which energy released by moving a driving ion (K+ or Na+) down its gradient and this is used to move a solute up its gradient. (Sometimes called cotransporters or secondary active transporters)

Who is credited with discovering penicillin?

Fleming

Can you think of an example of a microbe that has evolved metabolic capabilities to grow in a specialized ecological niche?

Gas vesicles or even having photosystems.

What structures do bacterial cells use for attachment?

Glycocalyx, fimbira and pili.

What are the key differences in the cell wall composition of gram negative and gram positive organisms?

Gram negative bacteria are bounded by two membranes, the plasma membrane and the outer membrane of the cell wall. Gram positive membranes have a thick peptidoglycan layer with teichoic acids in their cell wall. Gram positive layers don't always have glycerol chains.

Interference microscopy is useful in visualizing what feature(s) of an object?

Helpful in defining shapes

What role does the high affinity binding protein play in the ABC transport system?

High specificity for binding and binds tightly to things it wants to bind to.

What are the three main components of the bacterial flagella?

Hook, filament, basal body.

How is energy stored in microbial cells?

In atp and proton motor force?

What is the bacterial nucleoid and how does it differ from the eukaryotic nucleus?

Irregularly shaped region within the cell of a prokaryote that

What role does lipoprotein play in connecting the outer membrane and the peptidoglycan layer?

It covalently links the two with fatty acids anchoring the lipoprotein to the inner membrane.

What are the various growth stages in a batch culture growth experiment? What physiological events are occurring in each stage?

Lag phase, log phase, stationary phase, death phase.

How do microbes obtain energy?

Light or chemical energy

What distinguishes a Lithotroph from an Organotroph?

Lithotrophs use inorganic molecules rather than organic molecules.

What molecules make up an organism's domain? what are some types of genetic material? and what do they tell us?

Millions, or even billions of base pairs. The genes in a microbe's genome and the sequence of DNA tell us a lot about how that microbe grows and associates with other species. Chromosomes, plasmids, prophages (viruses).

What molecules are transported by the group translocation systems? What parts of the system are general and which are specific? How is energy provided to the system?

Mostly sugars as it gets phosphorylated. E1 is general and E2 is specific.

What advantage(s) do gas vesicles provide to phototrophic organisms? Could they benefit a non-phototropic organism?

Move closer to the surface due to buoyancy. They could, but probably not (oxygen dependent organisms).

Is a virus a microbe

No, because a virus is a noncellular particle containing genetic material that takes over the metabolism of a cell to generate more virus particles. Some viruses consist of only a short chromosome packed in protein. Other kinds of viruses, such as Pandoraviruses that infect amebas, show the size and complexity of a cell. Although viruses are not fully functional cells, some viral genomes may have evolved from cells. Additionally, it cannot reproduce by itself and is dependent on a host.

What is the energy source for the flagellar motor?

PMF - Proton Motive Force - separation of charge and pH across the plasma membrane - protons moving down their gradient

What are passive diffusion, facilitated diffusion and active transport? Which are mediated by proteins?

Passive Diffusion: Movement across a membrane with no energy input and no assistance from a protein Solutes follow their concentration gradiet, flowing from high concentration to low concentration. Facilitated Diffusion: Solutes move across a membrane, from high concentration to low concentration. Cannot move solutes against their gradient. Mediated by a protein Active Transport: Requires the input of energy to move solutes. Can be either a coupled transport system or an ABC transporter. Moves solutes against their concentration gradient.

What antibiotics target the synthesis of peptidoglycan?

Penicillin, vancomycin, and bacitracin.

What is the main component of the bacterial cell wall? What are the sugar building blocks of the structure and how are the chains joined together? where is this made?

Peptidoglycan, Nacetylglucosamine and Nacetylmuramic acid, and they are joined by peptides cross-bridges (and sugares are connected by B-14 Linkage). Occurs outside of the cytoplasm.

What are the different types of flagella organization in bacterial cells?

Peritrichous cells have flagella randomly distributed around the cell. Lophotrichous cells have flagella at the end(s)-one or both end. Monotrichous cells have a single flagellum.

How do photons interact with objects and how are these different interactions used in microscopy?

Photons interact with objects in a variety of ways including absorption, reflection, refraction, and scattering.

What relationship is used to estimate the resolution of a lens in bright field microscopy?

R = ½ wavelength/NA

Why is resolution increased at lower wavelengths?

Resolution increases as theta (angle of aperture) increases. When theta increases, the NA (numerical aperture) increases. Higher NA = increased resolution.

How does septation differ for cocci and rods? What role does MreB play?

Rods are similar but elongate prior to septation and use an additional protein, MreB • MreB determines cell diameter and coordinates cell wall synthesis along the long axis as Z ring forms in center

What special properties of a fluorophore molecular are exploited in fluorescence microscopy?

Samples are stained and the wavelengths of excitation and emission are determined by the fluorophore

What specialized systems do bacterial cells use to acquire iron?

Siderophores

What is the function of the lens?

Slows and bends light

What unusual features of caulobacter's cell division cycle allow it to retain contact with the surface and produce free living cells?

Stalk and holdfast

What specialized structures does Caulobacter have that allow it to adhere to surfaces?

Stalks

What might be the consequences of loosing FtsZ activity?

The cell does not septate.

What two proposals changed our view about the five kingdom classification of Whittaker?

The endosymbiotic theory (Lynn Margulis) and Three Domain Classification (carl woese's theory)

What role does FtsZ play in septation and how does it locate the "center of the cell"?

The formation of membrane and cell material at the division septum. The formation of membrane and cell material at the division septum

What two processes are used by microbes to assimilate carbon to build biomass?

The heterotrophic and autotrophic cycle.

What is the generation time (g) and how does this differ from the specific growth rate?

The interval for the formation of two cells from one cell the change in cell number or cell mass per unit time

What does a higher NA mean

The numerical aperture goes up, increasing resolution

How are cryo-EM techniques used to construct 3-D images of cells?

The specimens are flash-frozen and suspended in water

What special features of mycobacterial cell walls make these organisms difficult attack with antibiotics?

Their envelopes are characterized by the presence of unusual lipids, mycolic acids, and unusual sugars, arabinogalactans

Based on the biochemical composition of an E. coli cell, what can we conclude from the observation that non-mRNAs are a larger fraction of the total weight of the cell than mRNAs?

There are lots of ribosomes in the cell Because they go through lots of transcription/translation.

What are the differences between simple and differential stains?

There are simple stains affecting all cells and differential stains for specific features or structures that can distinguish between different types of cells.

What conditions are necessary for electromagnetic radiation to resolve an object?

There must be contrast between object and its medium Wavelength of radiation must be smaller than the object Detector must have sufficient resolution for the given wavelength

Carboxysomes are members of what general class of structures? What types of reactions are frequently associated with these sub-cellular structures?

They are microcompartments which have co2 fixation via enzymes

Are archaeal cells that show gram-negative response going to have an outer membrane? Does it tell us anything about their membrane layer.

They often show themselves as gram negative but are not!

What fundamental traits are shared by most prokaryal organisms?

Thick outer envelope, compact genome, and tightly coordinated cell functions

Explain why the surface to volume ratio is important for bacterial growth. Should bacilli have faster growth rates than cocci?

To maximize chemical exchange and growth, A smaller ratio is better, resulting in faster growth, meaning bacilli should grow slower.

What are the two main types of electron microscopy and what cellular features are visual by these approaches?

Transmission Electron Microscopy - Electrons are transmitted through a specimen, revealing internal structures Scanning Electron Microscopy - Electrons scan a surface of specimen and are reflected to produce a 3D image - particularly useful for visualizing complex communities of cells

Who was credited with the development of enrichment culture Techniques?

Winogradsky

Does E. coli have a cell cycle?

Yes. even though dna synthesis does not stop which is different in prokaryotes.

What role do porins play in the outer membrane? Could they affect antibiotic sensitivity? What is the S-layer and where is it located?

allow small molecules and ions to enter, but the membrane acts as a barrier to large molecules and proteins • It creates a membrane-enclosed compartment bounded by the outer membrane and the cytoplasmic membrane called the periplasmic space. This can affect the antibiotic sensitivity. Another protective layer found in bacterial and archaeal organisms is a surface layer made of protein or glycoprotein

What are common morphologies and arrangements of microbial cells? What arrangements are indicated by Staphylo- Strepto- references.

another quizlet

How does Caulobacter crescentus cell division differ from E. coli?

asymmetrical cell division program that allows free living (stalked form) cells to propagate to produce both free living and attached cells.

What role does the signal recognition particle play in the synthesis of membrane proteins? Can this process be coupled to transcription? Could this happen in a eukaryal Cell?

binds to the growing peptide and delivers the translating complex to the membrane. No trasnlation in the nulear compartment for eukaryal cells. It is indirectly coupled because they all happen right next to each other.

Beyond its role in attachment, what other functions are associated with pili?

genetic exchange process called conjugation • others participate in a special type of motility called twitching motility

What are the general steps in the synthesis of peptidoglycan?

https://quizlet.com/274745197/peptidoglycan-synthesis-flash-cards/

If we assume that TipN interacts with PodJ, what might happen if TipN was absent?

it raises the question of does the cell even divide into two cells and will one be stationary and the other not?

What is the periplasmic space? What protein functions might be in this space?

membrane enclosed compartment bounded by the outer membrane and the cytoplasmic membrane. Peptidoglycan is made here.

What are the components of a phospholipid? What types of fatty acids are present and how might their structure affect membrane fluidity? How might it change in going from higher to lower growth temperatures.

phosphoryl head groups and their fatty acid side chains. Saturated decrease the fluidiy, and unsaturated, they increase the fluidity because they don't pack so tight. High to low temps of the membrane you want to increase the fluidity with more unsaturation/fatty acids since fluidity increases as temp increase.

What is chemotaxis and how do cells achieve a net movement toward attractants (or away from repellents)?

the movement of a bacterium in response to chemical gradients. (environmental gradients

What is defined minimal medium and how does it differ from a complex medium? Does complex always mean complicated?

those that contain the minimum nutrients possible for colony growth. Complex media are ones that also contain blood components.

What is meant by the statement that transcription and translation are coupled? Why doesn't this occur in eukaryal cells?

translation begins on the growing RNA chain before the transcription event is completed • Unlike eukaryotes, prokaryotes synthesize RNA and proteins continually while the cell's DNA undergoes replication.

How do archaeal lipids differ from those found in bacterial cells? Would you expect them to differ in their chemical sensitivities?

• Glycerol backbone • Lipids are branched terpenoids formed from isoprene units • Lipids are joined to the glycerol backbone through ether (C-O-C) linkages • Cyclopentane rings occur in some organisms • Tails can be linked to form a tetra-ether monolayer

How do the coupled transport systems, symport and antiport, differ from each other? Do either require ATP?

• In symport, the two molecules travel in the same direction. • In antiport, the actively transported molecule moves in the direction opposite to the driving ion.

What functions are typically associated with membrane proteins?

• Structural support connecting the layers or anchors for flagella • Communication with the environment: secretion systems and sensors • Transport of ions and nutrients and energy storage (proton motive force)