MIC 102 UC Davis

What is a microbe?

"free-living organisms so small that they are only visible under the microscope"

Are their exceptions to the definition to microbes?

Yes, some microbes are hug, not free-living, or organisms

What is LUCA? And how does it relate to microbes?

Last Universal Common Ancestor is thought to be what all organisms have evolved from over 4 billion years. Specifically though, the LUCA is thought to be a microbe. Can determine relationships from the small subunit (16S) rRNA gene

Name three characteristics of LUCA

The LUCA and common species today share 1) DNA as genetic material 2)Protein and RNA 3) Lipid Membrane

Explain how the three domain tree is different from the ring of life.

The three domain tree groups the organisms into their three appropriate lineage (Bacteria, Archaea, and Eukarya), Each developing linearly and separating with different adaptations. Whereas a ring of life includes lineage from lateral gene transfer - the organisms are really intertwined with one another and creating new species.

What are the pros and cons for microbes being small?

Pro: microbes can maintain a high surface-to-volume ratio to maximize nutrient exchange.

Con: Easy targets for larger microbes/species.

How does cell shape influence cell metabolism?

High surface are to volume ratio can increase metabolism of nutrients, which will in affect increase growth and reproduction.

Compare and contrast the general structures of archaea, bacteria and eukaryotic bacteria.

Prokaryotics: no nucleus

bacteria: have rod shaped, sphere shaped, and helixcal shapes

archaea: have sphereical and rod shaped organiams

Eukaryotes: have fungi, slime molds mircroscopic algae, and protozoa...Organelles include nuclus, mitcochondria, and chloroplast.

Explain why cells must have a membrane

To make a selective barrier for chemical diffusion and allow the primitive biological molecules to replicate and catalyze reactions in a protected , favored environment.

Provide evidence for two cases of convergent evolution between bacteria and archaea cell exteriors.

1. flagella, but they differ in their assembly and structure.

2. Pili: filamentous appendages, which will attach to host cells, transfer proteins and nucleic acids to other cells and motility.

Why must bacteria cells be stained to cell them?

Because it is hard to contrast the colorless cell and can;t be seen readily under the microscope. gram postive stains purple and gram negative will stain red.

List advantages and disadvantages of light microscopy, fluorescence microscopy, and electron microscopy.

-Light microscopy: pro can see the small microbes and structural makeup, cons need to gram stain the bacteria to differentiate the species, which will kill them

-fluorescence microscopy: pro can target components in the cell or tissues by using dye and emitting light at specific wavelength, con ?

-electron microscopy: pro can determine fine structural detail to make a 3D picture, con:distort structure because shot with electron/proton.

Compare and contrast the cell envelopes of gram negative and gram positive bacteria.

Gram Positive: have a thick cell wall/peptidoglycan layer then a cell membrane. Have teichoic acid and lipoteichoic acid.

Gram negative: have two outer membranes with a thin cell wall/peptidoglycan layer in the middle. Have lipopolysaccharide

What are some roles of the bacterial murein cell wall?

1. thicker walls limits the passage of hydrophobic compounds.

2. Act as amour, and structural support.

Differences and similarities in the bacterial and archaeal cell membranes.

The bacterial phospholipid bilayer has ester linkages, and two phospholipids (hydrophillic heads and hydrophobic tails with two fatty acid chains).

The archaeal cell membrane can have either a phospholipid bilayer or monolayer connected by ether linkages. The monolayer here however, with have 40 carbon isopreniod groups(one straight chain from the outsides)

Predict mechanisms that could allow gram positive bacteria to become resistant to penicillins.

Gram positive bacteria maybe could have developed thicker peptidoglycan layers, or have developed another enzyme that cross-links the layers together.

Differences and similarities in the bacterial and archaeal cell wall.

Archaea do not have murein cell walls and protect themselves with just an S-layer. Cell walls of archaea could be made up off pseudomurein (made up of polysasccarides or a type of peptidoglycan.) - these will also stain gram positive.

Importance of hopanoids for bacteria.

Hopanoids are unsual lipids made by only bacteria. These add rigidity and stability to the cell membrane. These are useful for detecting bacteria.

How can acid-fast bacteria can withstand membrane-damaging chemicals?

The cell walls contains large amount of waxes called mycolic acids (made of long, complex fatty acids). This robust, thick wall is hydrophobic, which are impervious to harsh chemicals/acid/soap. Con of this is that it slows down the nutrient uptake and growth.

Why would a bacteria or an archaea invest in making an S-layer when it already has a cell envelope?

The crystalline surface layer is anchored to murein cell wall of gram positive, to the out membrane of gram negative and to archaeal directly to cell walls or to cell membrane. The purpose is to act as an external layer of protection and can recrystallize on their own (self-assemble).

Describe three main functions of the structure and function of bacterial flagella.

Structure includes a basal body(complex structure. 15 proteins to make rings and a rod), a hook ("joint", made of a single protein, then a filament (helical, hollow, and singel protein).

They are synthesized from the bottom to top (body to filament.

There function is used for locomotion

Compare and contrast the composition and assembly of flagella and pili.

Flagella is synthesized from the bottom to top from single proteins. Moving by the joint

Pili are assembled from pilin moner into a helix. Moving comes from pushing something out and back in(twitch motility)...can also transfer genetic material to other microbes, and can attach with adhesions

Discuss how a slime layer allows cells to form biofilms.

A slime layer is a loose coat of slime (capsules are tenacious slime and attached to cells). The slime layers helps microbes adhere to surfaces and build multi cellular communities known as biofilms. Stick together.

What is the difference between gram positive and gram negative murein?

positive is thicker, negative is thin and in the middle of cell membraines. Also the positive has Glysine protein in the middle, whereas negative has DAP in the middle.

What are lipopolysaccharides? porins?

in gram negative, LPS = endotoxin when cells dies.. porins are specific protein channels.

What is the periplasm?

10nm space in between inner and outer membrane and houses both proteins and cell wall.

What are mycoplasmas?

Cells that have no cell wall(peptidoglycan layer), but use sterols in membranes to make more rigid and preserve integrity. Hard to kill by drugs and small and spread fast.

Whats a consequence for B and A of having DNA in the cytoplasm rather than is a necleus?

Its good because transcription and translation can occur together. Its bad maybe because it could be easily destroyed or less room for other gadgets.

Describe how DNA is packed and folded tightly inside nucleoids.

Supercoiling: cells of already twisted DNA. This process needs DNA gyrase to cut double helix and introduce regulative supercoils and topoisomerase 1 to make single strand break and relax the negative supercoil. Cations also bind to it to neutalize its intrinsic negative charge.

What are three benefits to having cell crowding in bacterial cytoplasm?

aids protein folding, promotes interaction between protein and chaperiones, and transcription/translation to occur quickly after one another.

Compare and contrast carboxysomes to enterosomes.

Carboxysomes = fix co2

Enterosomes = do not fix co2

have the same structures though

Function of gas vesicles

aquatic photosynthetic bacteria, will hold gas products in a protein shell to increase bouancy.

Function of Thylakoids

To increase light-gathering abilities of photosynthesis bacteria by increase the surface area (double membraned)

State a benefit and a potential drawback for a bacterium hosting magnetosomes.

Benefits: move without energy

Drawback: need to reply on external source for motility

What does growth of a microbe mean?

Either cells getting bigger or populations increasing by binary fission.

Learn the usefulness of measuring microbial growth with turbidity, viable cell count and total particle counts.

- turbidity: measuring amount of mass within a culture..light more scattered the more mass, and will e more accurate with freshly grown cultures

-viable cell count: counting colonies..

-direct cell count: counting cells..cant really determine dead versus alive

-flow cytometry: count cells with lazer.

Describe what microbial cells are doing during each of the four phases of growth.

1. Lag phase: adjusting to new environment

2. Exponential growth: growth at a constant rate

3. stationary phase: cells not activily growing

4. Death phase: cell growth lowers exponentially

5. up and down: some will survive and remian semistable.

Calculate the number of generations, generation time, and specific growth rate for a given culture.

N=N0 X 2^n

n=(log(N) - log(No))/0.301

g=t/n

N=population

N0=initial population

n=number of generations

What is balanced growth?

It is expotential growth and it is staying in that phase. Cell composition increases by the same proportion, mean cell size is constant, requires unchanging environment, low cell density. by chemostat

Describe how very high and very low temperatures, pH, and salt concentration inhibit growth.

Low temps: specialized proteins and adjusted fatty acid composition

high temps: protein denature, or other shit.

pH? no idea

salt concentrations: decreases water activity, and lowers cell turgor.

Explain in general terms what a chemostat is and what it is used for

It is a device to allow continuous balanced growth through constant dilution. rate of addition of medium determine growth rate. density of cells kept constant because of a limmiting nutrient.

Describe how FtsZ and Min proteins interact to cause cell division along the midline.

FtsZ will form a ring, Min CD moves back and forth from each poly and polymerizing, Min E diffuses freely and prevents Min CD from polymerizing the middle. this will help the FtsZ ring shrink at the middle.

Describe how mutations in fts or min genes affect cell division.

will cause non-symmetric division: budding, stalked, or swammer cell.

Apply these terms to metabolic lifestyles: Photo/chemo, litho/organo, auto/heterotroph.

-Energy source: light=photo, chemical=chemo

---litho=inorganic, organo=organic

-carbon source: organic=hetero, inorganic=auto

-electron source: auto

Diagram the overall scheme of metabolism, identifying the pathways that consume and produce energy. Explain for which pathways prokaryotes exhibit high levels of diverity.

Fueling growth to

Precursor metabolites (made from inital carob and energy sources. Energy/reducing power generated) to

Building Blocks (fatty acids, sugars, amino acids, nucleotides to

Macromolecules (are polkymerization except lipids. Consume energy) to

Cell structures

Compare and contract ATP generation by transmembrane ion gradients and substrate level phosphorylation with respect to the mechanism of ATP generation and number of ATPs generated.

SLP: ATP is made from harvesting the energy in the phosphorylized bond that was energized by NAD to NADH.. 2 ATP molecules made per one glucose molecule

Ion gradients: ATP synthase produces ATP by pushing H+ from the proton motive force (this gradient was made by ETC) into the cell. 3-4 H+ for one molecule of ATP

Explain how NAD+ is regenerated during metabolism and why its regeneration is so important.

NAD+ can be regenerated by fermentation. NADH produced by glycolysis is used to reduce pyruvate and its derivatives, forming fermentation products distinct for each organism.

List the key elements and functions of transmembrane ion gradients. Predict the the impact on a cell from: permeabilizing the membrane (e.g.: with a detergent or antibiotic polymyxin) or adding a drug that blocks the transfer of electrons between the ETC (e.g.: rotenone)? What is a PMF, and how is it connected to ATP?

Key elements include the electron transport chain and the proton motive force (high protons on the outer membrane, which helps drive ATP synthase). If the membrane become more permeable, there would be a lower PMF...If the ETC was not working, there would be no PMF, which will affect respiration and photosynthesis.

Explain how energy is generated during photosynthesis, and what the electron sources are.

solar energy to chemical energy. Electrons come from electron donors, like water, lactate, reduced sulfur compounds, or many substrates.

Describe the role of cyanobacteria in the oxygenation of the planet.

Cyanobacteria were the first that produced O2 and basically suffocated the other microbes.

What is fermentation?

What is respiration?

What is photosynthesis?