Official Study Guide- Exam 1

The interactions of microbes among themselves and with their environment are determined by their metabolic abilities: Identify 2 strategies microbes use to obtain building locks, such as essential AA's from exogenous sources.

1- Fueling: ~living-organisms= can create order from their disordered environment. ~the fueling reactions that generate the 13 precursor metabolites are energy (ATP and reducing power) for biosynthesis can be conveniently divided into 3 stages a. first, the substrates that are available in the environment enter the cell either by passive diffusion through the cell envelope layers or by active transport using specialized transport proteins. b. second, both heterotrophs and autotrophs use feeder pathways to generate the intermediate organic molecules needed for central metabolism. c. third, to make the core precursor metabolites. 2- Biosynthesis: ~if it cannot acquire them from the environment, it must make them using the 13 precursor metabolites ~glycolysis generates several precursor metabolites needed to make sugars, AA's, and FA's. It also feeds metabolites to the pentos-6-phosphate pathway which makes the precursor metabolites needed to make nucleotides and some AA's.

Describe 3 ways in which membranes have adapted to confer survival in some harsh environments.

1- Glycerol diether linkages (vs. more easily hydrolyzed glycerol diester linkages) 2- 20 carbon isoprenoid groups (vs. fatty acids) 3- Covalent link the 20 carbon isoprenoid groups - essentially this means that there is no bilayer anymore and therefore the membrane would be more stable

List the 2 most common elements in a typical bacterium.

2 most common elements: ~carbon (~50%) ~oxygen (~20%) Total elements in a typical bacterium: ~carbon ~oxygen ~nitrogen ~hydrogen ~phosphorus ~sulfur ~others

List the 2 most abundant macromolecules in a typical bacterium?

2 most common macromolecules: ~protein ~RNA Total macromolecules in a typical bacterium: ~proteins ~RNA ~DNA ~lipids ~carbohydrates

Give examples that exemplify how the human microbiota are well adapted to their microenvironments.

Ex 1- they are able to benefit from the microbes around them to benefit the host. Ex 2- They can identify certain microbes that are foreign, and will try to compete with them for the spot they occupy. Ex 3- they are able to reproduce at great numbers.

Bacteria range in volume over 1-million-fold. Discuss some of the consequences of being much larger or much smaller than the average E. coli cell. What does being small allow a microbe to do? What can a microbe do if it has a large volume and not a large surface area? What happens as cells grow larger? For cells to keep their metabolism functioning at the highest possible rate to grow and reproduce quickly, what must cells do? What is the rate that rapidly growing microbes process their nutrients? Why is this important? Why does rapid chemical turnover have significant consequences? What is high volume-to-surface ratio particularly important to?

Advantages: ~being small allows microbes to maintain a high surface area-to-volume ratio to maximize chemical exchanges and growth. ~it is possible for microbes to compensate for their large volume by increasing their surface area (such as folding the outer membrane) ~as cells grow larger, their volume increases rapidly compared to the surface area and the rates of chemical exchange (such as nutrients diffusing in and waste diffusing out) ~to grow and reproduce quickly, cells must exchange chemicals efficiently with their surroundings. ~microbes process their nutrients at a rate of 10-1,000 times higher per gram than mammalian cells. With small increases in size, a big difference can be noted with chemical diffusion and even cell growth. ~rapid chemical turnover= has significant consequences b/c one can get sick with an infection (such as bacterial) very quickly b/c the infective cells grow at great rates before our immune system is able to eliminate the threat. ~high surface-to-volume ratio= particularly important for microbes that are in an environment where competition for nutrients is high.

Bacteria and Archaea have specialized structures (such as flagells, endospores, etc..) that often confer critical capabilities: Compare and contrast the lipid membranes in Bacteria and Archaea

Bacteria: ~Phospholipid bilayer (hydrophilic head/hydrophobic tail) ~Favors the more spontaneous reaction of bilayer Archaea: ~Glycerophosphate head attached to isoprenoids (instead of fatty acids) ~Uses ether bonds (instead of ester)

List 4 cell functions that require energy for growth related and growth independent.

Cell functions that require energy: For Growth Related: 1- nutrient entry 2- biosynthesis of building blocks 3- polymerization of macromolecules 4- modification and transport of macromolecules 5- assembly of cell structures 6- cell division For Independent Growth: 1- motility 2- secretion of proteins and other substances 3- maintenance of metabolite pools 4- maintenance of turgor pressure 5- maintenance of cellular pH 6- repair of cell structures 7- sensing the surroundings 8- communication among cells

Compare and contrast ATP generation by transmembrane ion gradients and substrate level phosphorylation with respect to the mechanism of ATP generation and number of ATP's generated: For chemoheterotroph, photoheterotroph, chemoautotroph, photoautotroph, and chemolithotroph: What is their source of energy? What is their source of carbon? What is their habitat?

Chemoheterotroph: ~energy= organic compounds ~carbon= organic compounds ~habitat= most animals Photoheterotrophs: ~energy= sunlight ~carbon= organic compounds ~habitat= green, non-sulfur Chemoautotrophs: ~energy= inorganic chemicals (H2S, S, Fe) ~carbon= CO2 ~habitat= hydrogen sulfur bact. Photoautotrophs: ~energy= sunlight ~carbon= CO2 ~habitat= lands (for plants) Chemolithotrophs: ~energy= inorganic compounds ~carbon= CO2 ~habitat= ?

Microbes are ubiquitous and live in diverse and dynamic ecosystems: Identiy an example species that is a chemoheterotroph and one that is a photoheterotroph.

Chemoheterotroph: organisms that obtain energy by the oxidation of electron donors in their environment. Use inorganic energy sources to synthesize organic compounds from carbon dioxide. Are unable to utilize carbon dioxide to form their own organic compounds. 1. extremophiles, bacteria or archaea that live in hostile environments (such as deep sea vents) and are the primary producers in such ecosystems. a. Chemoautotrophs generally fall into several groups: methanogens, sulfur oxidizers and reducers, nitrifiers, anammox bacteria, and thermoacidophiles. 2. sulfur-oxidizing bacteria, nitrogen-fixing bacteria and iron-oxidizing bacteria. Cyanobacteria are included in the nitrogen-fixing bacteria that are categorized as chemoautotrophs. Photoautotroph: use a light as a source of energy and carbon dioxide as their chief source of carbon 1. photosynthetic bacteria (green sulfur and purple sulfur bacteria and cyanobacteria) 2. algae 3. green plants

Describe how the habitats of chemoheterotrophs and photoautotrophs might differ.

Chemoheterotrophs: 1. are able to thrive in very harsh environments, such as deep sea vents, due to their lack of dependence on outside sources of carbon other than carbon dioxide. Photoautotrophs: 1. Organisms that carry out photosynthesis. 2. Using energy from sunlight 3. CO2 and H2O are converted into light organic materials to be used in cellular functions such as biosynthesis and respiration. 4. especially important in aquatic ecosystems. 5. Algae are photoautotrophs found in most ecosystems, but they generally are more important in water-based, or aquatic, ecosystems. Like plants, algae are eukaryotes that contain chloroplasts for photosynthesis.

While microscopic eukaryotes (fungi, protozoa, and algae) carry out some of the same processes as bacteria, many of their cellular properties are fundamentally different: Identify the difference in location of respiration b/w eukaryotes and prokaryotes.

Eukaryotic Respiration: ~respiration takes place in the in the mitochondria ~H+ protons are going to flow from the inter-membrane space to the mitochondrial matrix ~glycolysis= occurs w/in the cytoplasm ~krebs/TCA cycle= occurs in the mitochondrial matrix ~ETC= occurs in the inner mitochondrial membrane Prokaryotic Respiration: ~ respiration takes place in the cytosol ~H+ protons flow from the outer membrane into the cytoplasm ~all steps of cellular respiration= occur in the cytosol

Compare and contrast the cell envelopes of gram (-) and gram (+): What do they have in common, and what is different b/w them?

Common: ~cell wall is made of peptidoglycan (NAG and NAM) Differences- Gram (-) Bacteria: ~gram (-) bacteria have a outer membrane while gram (+) bacteria do not. ~the membrane= reduces permeability and nutrient uptake which would slow growth (to fix this problem= the outer membrane has porins to compensate) ~the outer membrane has additional proteins that translocate these compounds ~outer membrane= allows for the passage of small hydrophilic nutrients- which excludes hydrophobic compounds (small or large) and allows the specific entry of larger hydrophillic molecules it may need ~Cell envelope is unique because they surround the peptidoglycan cell wall with an outer membrane that is chemically distinct from all other biological membranes and is especially resistant to harmful chemicals ~Bacterial envelope has an inner leaflet composed of customary phospholipids, and its outer leaflet contains LPS (lipopolysaccharide) - LPS is a lipid modified with sugar; consists of one glycolipid (lipid A) and 1 or 2 sugar portions (LPS core and O antigen) ~Gram - cell envelope leaves an aqueous space b/t the inner and outer membrane → periplasm. The periplasmic compartment contains the peptidoglycan cell wall and a gel-like soln of cell wall precursors and proteins that assist in nutrition. There are degradative enzymes (phosphatases, nucleases, and proteases) that break down molecules to sizes small enough to be transported across the inner membrane. It contains proteins with high binding affinity for specific sugars and AA that egypt the cell to soak up nutrients from the medium. Also contains enzymes beta-lactamases which protect the cell by inactivating ATBs (penicillins and cephalosporins) Differences- Gram (+) Bacteria: ~have a thicker cell wall (murein) than Gram (-) ~The presence of the AA lysine (rather than the diaminopimelic acid/DAP of Gram - walls) is the distinctive chemical feature of all Gram + cell walls ~The many layers of peptidoglycan enriches for polar molecules such as phosphates, sugars and charged AA - resulted cell wall forms a thick polar barrier that limits the passage of hydrophobic compounds (ie: bile salts in the intestine). ~Cell wall contains teichoic acids - chains of glycerol phosphate or ribitol phosphate lined by a phosphodiester bonds and bound covalently to the peptidoglycan cell wall - the chains give rigidity to the cell wall but also change the chemistry of its external face promoting adherence of bacteria to specific surfaces. ~They do not have a periplasmic compartment so they secrete all these enzymes into the environment.

Describe how DNA is packed and folded tightly inside nucleoids: What is associated with genome storage? What is associated with transcription?

For Genome Storage: ~Super Coiling= reduces the amount of space and allows for DNA to be tightly packed (length of 1 DNA= can be greater than the length of the cell) ~DNA Binding Proteins= Proteins with DNA binding sites that have a specific affinity for single or double stranded DNA. For Transcription: ~Topoisomerase= it is a type of enzyme that relieves torsional strains in DNA. Removes (+) supercoils that is generated in front of the replication fork. Removes (-) supercoils that are generated downstream of RNA polymerase. ~DNA Gyrase= a bacterial enzyme that catalyzes (-) supercoiling of plasmid and chromosomal DNA.

Review the major differences b/t chemoautotrophs and chemoheterotrophs during respiration.

For chemoheterotrophs: 1. Intertwine their C and energy metabolisms because they can harness energy from the substrate that serves as the carbon source For chemoautotrophs: 1. Fix CO2 and make precursor metabolites use vast amounts of energy or reducing power 2. Some autotrophs rely on respiration to energize CO2 fixation; they freed the e- to the ETC directly from the inorganic chemicals → chemolithotrophs - and generate a p+ motive force to make ATP 3. When needed, chemoautotrophs use the energy in the p+ notice force to pump the p+ back inside the cell and reverse the flow of e- in the ETS, thus generating reducing power. 4. Most carry out aerobic respiration (use oxygen as the terminal e- acceptor) but some do anaerobic respiration

When comparing and contrasting b/w the cell envelope of gram (+) and gram (-) microbes: What should we know about- The peptidoglycan? The teichoic acid? The LPS (lippolysaccharides)? The proteins content The releasing of endospores? The thickness of the cell wall The outer membrane? The porin proteins? The permeability of molecules? ~look at diagrams for gram (+) and gram (-) bacteria in LO week 2- google docs

Gram (+): ~peptidoglycan= thick ~teichoic acid= present ~LPS= absent ~protein content= absent ~release of endospores= no ~thickness of cell wall= 20-80 nm ~outer membrane= absent ~porin proteins= absent ~permeability of molecules= more permeable Gram (-): ~peptidoglycan= thin ~teichoic acid= absent ~LPS= present ~protein content= present ~release of endospores= yes ~thickness of cell wall= 10 nm ~outer membrane= present ~porin proteins= present ~permeability of molecules= less permeable

Bacteria and Archaea exhibit extensive and unique metabolic diversity (nitrogen fixation, methane production, anoxygenic photosynthesis): Look at the difference in class, source of carbon, and source of energy.

Heterotroph Class: ~chemoheterotrophs source of carbon= organic compound source of energy= organic compound ~photoheterotrophs source of carbon= organic compound source of energy= light Autotroph Class: ~chemoautotrophs source of carbon= CO2 source of energy= inorganic compound ~photoautotrophs source of carbon= CO2 source of light= light ~Chemoheterotroph: use complex organic molecules as their carbon and energy sources. Energy course → use electrons from hydrogen atoms in organic compounds. Examples: most bacteria; all fungi, protozoa, and animals ~Photoheterotroph: use light as an energy source and an organic compound for their carbon source and electron donor (cannot convert carbon dioxide to sugar) - anoxygenic - examples: green nonsulfur bacteria & purple nonsulfur bacteria ~Chemoautotroph: Utilize inorganic molecules (H2, CO, NH3, NO2, H2S, S S2O32-, and Fe3+) as their source of energy and reducing power. Because of the inorganic nature of the chemicals used as energy sources these autotrophs are also called lithotrophs (stone eaters). Source of carbon → carbon dioxide ~Photoautotroph: use a light as a source of energy and carbon dioxide as their chief source of carbon. Examples: photosynthetic bacteria (green sulfur and purple sulfur bacteria and cyanobacteria), algae, and green plants - oxygenic

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

Light Microscopy: ~advantage= easy to use, inexpensive, can look at live specimens ~disadvantages= viruses, molecules, and atoms cannot be seen Fluorescence Microscopy: ~advantage= allows for detection of any protein or antigen of interest. Everything in the background is completely dark with the exception of the fluorophore tagged antigen, so it is easily detected. ~disadvantage= the photobleaching and that the specimen cannot be focused for a long time at high magnification. Electron Microscopy: ~advantages= magnificcation and higher resolution- as electrons rather than light waves are used, it can be used to analyze structures which cannot be seen by the naked eye. Resolution= in the range of 0.2nm, which is 1000x more detailed than light microscopy. It also has diverse applications and high-quality images are produced ~disadvantages= samples typically treated with strong chemicals that cross link the biological molecules to preserve the cells structural features during examination, this treatment can introduce artifacts as well- to avoid this you have to freeze the cells at temps that are so low that ice crystals cannot form in the sample

Describe an organisms relationship to oxygen based on its pattern of growth: For aerobe (strict aerobe), anaerobe (strict anaerobe), facultative (aerobe and anaerobe), and indifferent (aerotolerant anaerobe): Do they grow in the air? Do they grow w/out oxygen? Do they possess catalase and superoxide dismutase? What is their description? What are some examples for each?

Looking at Aerobe (strict aerobe): ~grow in the air= yes ~grow w/out oxygen= no ~posses catalase and superoxide dismutase= yes ~description= requires oxygen; cannot ferment ~examples= Mycobacterium tuberculosis, Pseudomonas aeruginosa, Bacillus subtilis Anaerobe (strict anaerobe): ~grow in the air= no ~grow w/out oxygen= yes ~posses catalase and superoxide dismutase= no ~description= killed by oxygen; ferments w/out oxygen ~examples= Clostridium botulinum, Bacteroids melaninogenicus Facultative (aerobe and anaerobe): ~grow in the air= yes ~grow w/out oxygen= yes ~posses catalase and superoxide dismutase= yes ~description= respire w/ oxygen; use anaerobic respiration or fermentation when oxygen is absent. ~examples= E. coli, Shigella dysenteriae, Staphylococcus aureus Indifferent (aerotolerant anaerobe): ~grow in the air= yes ~grow w/out oxygen= yes ~posses catalase and superoxide dismutase= yes ~description= respire w/ oxygen; use anaerobic ferments w/ or w/out oxygen ~examples= Streptococcus pneumoniae, Streptococcus pyogenes

Compare and contrast the total catabolic ATP yield for an organism using aerobic and anaerobic respiration and fermentation: First, comparing aerobic and anaerobic respiration, Does it use oxygen? What is produced? How many ATP are produced per glucose molecule? What is respiration controlled by? What are the steps for each? What type of organisms conduct aerobic and anaerobic respiration? What type of phosphorylation is used to generate ATP? For fermentation: What is the growth condition? What is the final hydrogen (electron) acceptor? What is the reduced product that is formed? What type of phosphorylation is used to generate ATP? How many ATP molecules are produced for every one glucose molecule?

Looking at Aerobic Respiration: ~oxygen= used ~product= CO2 and H2O ~ATP= 38 molecules produced in prokaryotic aerobic, and 36 molecules produced in eukaryotic aerobic. ~respiration= controlled by enzymes ~steps= glycolysis (including EMP), pyruvate oxidation, TCA/Krebs cycle, electron transport chain ~mostly all organisms= aerobic respiration ~phosphorylation used to generate ATP=oxidative and substrate level phosphorylation. Looking at Anaerobic Respiration: ~oxygen= not used ~product= lactic acid, CO2, H2O ~ATP= varies, but greater than 2, and less than 38 molecules produced ~respiration= controlled by enzymes ~steps= glycolysis, TCA cycle, ETC ~seen in plants and animals ~phosphorylation used to generate ATP=oxidative and substrate level phosphorylation. Looking at Fermentation: ~growth condition= aerobic or anaerobic ~final hydrogen (electron acceptor)= an organic molecule such as pyruvic acid ~reduced product that is formed= ethanol, lactic acid, butyuric acid, etc. ~phosphorylation used to generate ATP= substrate level phosphorylation (SLP) ~For every glucose molecule= 2 ATP's are produced

Compare and contrast cyclic and non-cyclic photosynthesis.

Looking at Cyclic: ~The e- acceptor is the same chlorophyll that was photoexcited ~By accepting back the e- the chlorophyll returns to the ground state and it is once again ready to initiate a new round of photoactivation and e- transport ~To make the reducing power for biosynthesis, these phototrophs can reverse the e- transport at the expanse of the proton notice force ~Carry out anoxygenic photosynthesis b/c they recycle the e- back to the chlorophyll Looking at Non-cyclic: ~E- do not return to the light-sensitive pigment but flow to NADP+ to make reducing power ~The reducing power can then be used for biosynthesis while any excess can be used to boost the transmembrane proton gradient and generate ATP ~This one way street creates a problem → once the light sensitive pigment in the reaction center transfers the e- to the first ETS carrier, it cannot start a new cycle of excitation ~The chlorophyll needs an e- donor to replenish the missing e- bringing the pigment back to its ground state ~Non cyclic phototrophs have diversified their metabolism to use a variety of e- dontors a. Some use inorganic e- donors (H, S, Fe2+) b. Cyanobacteria use H2O as an electron donor and generate O2 as a byproduct - b/c O2 is released these microbial phototrophs are said to carry out oxygenic photosynthesis

The structure and function of microorganisms have been revealed by the use of microscopy (including bright field, phase contrast, fluorescent, and electron): Identify 3 ways in which prokaryotes and eukaryotes are structurally different.

Looking at Prokaryotes: 1- smaller than eukaryotes (this allows them to increase their volume-to-surface area ratio, and its max diffusion of nutrients and waste products). 2- have a cell envelope (defined by gram (-) and gram (+) staining. 3- have fatty acid chains that are not branched (20-40 carbons depending on it being a monolayer or bilayer (this is used by archaea and bateria is bilayer For eukaryotes: 1- have a cytoskeleton while prokaryotes polymerize proteins to make a skeletal framework that is similar. 2- have a nucleus where as prokaryotes have a nucleoid 3- have organelles while prokaryotes don't.

Speculate on why membrane proteins are more abundant in Bacteria and Archaea than in mammalian cells?

Prokaryotes (Bacteria and Archaea): ~they only have a cytoplasmic membrane ~all membrane proteins expressed by prokaryotes must be present only in the cellular membrane Eukaryotes (mammalian): ~they have a cytoplasmic membrane and membranes that surround every organelle ~membrane proteins can be expressed of the membranes of the organelles, and not just the cellular membrane

Why are viruses not considered microbes? a. they are smaller than 1 micrometer b. they do not remain intact during replication c. they require host cells to grow d. they lack nucleic acids to store genetic information e. they must possess lipid membranes

b. they do not remain intact during replication c. they require host cells to grow

When thinking about what's inside of the cell membrane of prokaryotes, what should we know about each of its functions: The nucleoid? What is its function? The cytosol? What is its function? The vesicles (in some only)? What is its function? The storage granules (in some only)? What is its function? The magnetosomes? What is its function?

The nucleoid- ~repository of genome ~transcription The cytosol- ~polyribosomes= protein synthesis ~enzymes= metabolism ~regulatory proteins= regulation of gene expression ~metabolites, precursors, energy compounds, salts= participate in metabolism ~cytoskeleton= chromosome segregation and cell division The vesicles (in some only)- ~gas vesicles= cell buoyancy ~photosynthetic vesicles= photosynthesis ~chemosynthetic vesicles= chemosynthesis ~carboxysomes= enhance CO2 fixation in heterotrophs ~enterosomes= metabolism of propanediol, others The storage granules (in some only)- ~acidocalcisomes= storage energy-rich compounds: polyphosphates, PHA's ~others= glycogen-like compounds, sulfur compounds Magnetosomes= involved in directional orientation with respect to magnetic field

Which of the following is not true regarding DNA supercoiling in the prokaryotic chromosome? a. it helps pack the DNA in the small space of the nucleoid. b. too much supercoiling induces the synthesis of DNA gyrase. c. it lowers the energy to separate the two DNA stands. d. supercoiling is possible because the prokaryotic. chromosome is circular.

b. too much supercoiling induces the synthesis of DNA gyrase. ~Excess supercoils generated by gyrase are removed by topoisomerase enzymes, which make single-strand breaks in DNA that relax the supercoils. Synthesis of DNA gyrase is induced by too few supercoils (or positive supercoiling).

In the redox fueling reaction, Succinate + NAD ↔ Fumarate + NADPH, the succinate molecules is undergoing which process? a. Reduction b. Catalysis c. Oxidation→ Succinate provides electrons to form the reduced molecule NADPH from the oxidized molecule NAD, so it is oxidized. d. Protein synthesis Glycolysis

c. Oxidation ~Succinate provides electrons to form the reduced molecule NADPH from the oxidized molecule NAD, so it is oxidized. Protein synthesis

Which of the following statements comparing and contrasting heterotrophs and autotrophs is NOT true? a. Both heterotrophs and autotrophs synthesize precursor metabolites b. Heterotrophs use organic C sources as energy sources whereas autotrophs use CO2 only c. Heterotrophs cannot be phototrophs d. Heterotrophs and autotrophs can harness energy from light.

a. Both heterotrophs and autotrophs synthesize precursor metabolites ~Autotrophs synthesise their own food using sunlight and carbon dioxide. They can synthesize all the precursor molecules themselves. Heterotrophs obtain glucose, lipids and amino acids from other organisms or different sources.

Order the following macromolecules account to the energy a typical prokaryote cell consumes for its biosynthesis, from highest to lowest: Highest (1) → Lowest a. DNA b. RNA c. Proteins d. Glycogen e. Phospholipid

a. DNA (4) b. RNA (2) c. Proteins (1) d. Glycogen (5) e. Phospholipid (3)

Which of these is not found in any prokaryotic cell? a. Plasmids that are stably inherited b. Storage granules containing DNA c. Circular DNA with regulated supercoiling d. Coexisting thylakoids and carboxysomes e. Gas vesicles and carboxysomes surrounded by protein shells

b. Storage granules containing DNA ~Different bacteria use storage granules as repositories for sulfur, calcium, phosphate, or carbon, often in polymeric form.

Methanogens are a group of anaerobic Archaea that gain energy from growth using H to reduce CO2 and generate methane. How would you classify this organism? a. Chemoheterotroph b. Chemoautotroph c. Photoheterotroph d. Photoautotroph

b. chemoautotroph

You have isolated a new organism that is small coccus and stains purple in a gram stain. Based on this, you can conclusively identify the cells as? a. bacteria b. gram (+) bacteria c. gram (-) bacteria d. acid-fast bacteria e. none of the above

b. gram (+) bacteria ~stains purple because the cell wall is thick consisting of several layers of murein (a type of peptidoglycan) that retains the complex purple dye and iodine after a brief alcohol wash

Glucose fermentation by some microbes results in the accumulation of acids such as acetate and lactate in the medium. The acid byproducts are necessary to a. increase ATP production by substrate level phosphorylation b. increase ATP production by respiration c. achieve redox balance d. reverse electron transport to generate reducing power e. disrupt energy transport

c. achieve redox balance ~The redox reaction is one in which one substance loses electons and the other substance gains them. eg. during the conversion of lactate to pyruvate, lactate loses its two electrons and convert into pyruvate whereas, NAD+ accepts two electrons and become reduced to NADH.

Microbes are ___. (select the best answer) a. relatively small b. microscopic c. free-living d. unicellular e. prokaryotes

c. free-living

In which condition are the isoprenoid bilayers of archaeal cell membranes NOT more stable than phospholipid membranes? a. high temperature b. high salt concentations c. neutral pH d. low pH

c. neutral pH ~isoprenoid bilayers (particularly the monolayers) are more stable than the phospholipid membranes at low pH and at high temperatures and salt concentrations making them the membrane choice for heat loving archaea

An enrichment culture a. promotes the growth of the most abundant microbe in a sample. b. promotes the growth of a particular taxonomic group. c. promotes the growth of microbes with a particular metabolic trait. d. is a pure culture.

c. promotes the growth of microbes with a particular metabolic trait.

What keeps the DNA in a prokaryotic cell nucleoid in an organized and condensed form? a. nuclear envelope b. cations c. riobosomes d. DNA-binding proteins

d. DNA-binding proteins ~Cations bind and neutralize the negatively charged DNA, allowing DNA-binding proteins to condense the genome by folding the DNA strands into loops

The cellular reducing power of NADH and NADPH is used to generate a. precursor metabolites b. macromolecules c. ATP d. all of the above

d. all of the above

How is the prokaryotic nucleoid different from the eukaryotic nucleus? a. It is condensed b. it is supercoiled c. it is circular d. it lacks a membrane boundary.

d. it lacks a membrane boundary. ~Unlike the eukaryotic nucleus, the prokaryotic nucleoid is not separated from the cytoplasm by a membrane. All chromosomes—prokaryotic or eukaryotic—are condensed and supercoiled to pack the genomes inside the cells. Although most prokaryotic chromosomes are circular and most eukaryotic chromosomes are linear, there are exceptions on both sides.

Microbes provide essential models that give us fundamental knowledge about life processes: List 2 reasons why E. coli is a model organism for growth metabolism.

~A lot is known about e. Coli's genome ~The size and metabolic complexity is average compared to other bacteria

Describe the process of ATP generation by F1F0/ATP synthase

~ATP synthase derived from its 2 protein components (F1 and F0) ~The F0 component has an open cavity that takes in the p+ (or other ions) and a lower portion that rotates in response to the spontaneous movement of p+ down the concentration gradient across the membrane (The rotation activates the cytoplasmic F1 component so it can bind and phosphorylate ADP to make ATP) ~The ATP synthase energizes ATP synthesis from the flow of protons ~3-4 protons must pass through the ATP synthase to generate 1 molecule of ATP ~F1F0 ATP synthase can work in the opposite direction, hydrolyzing ATP and driving discharge of protons. ~When the electrochemical H+ gradient is favorable, F1Fo catalyzes ATP synthesis coupled to spontaneous H+ flux toward the side of the membrane where F1 protrudes.

Describe the role of ATP and NADH for an organism growing via fermentation.

~ATP= provides the energy that is needed for a microbe to maintain function and reproduce. ~NADH= allows for pyruvate to be converted to lactic acid (as NADH used, it is converted back to NAD+) ~NAD+= allows for glycolysis to continue

Compare and contrast aerobic and anaerobic respiration with respect to electron acceptor diversity and energy yielded during respiration.

~Aerobic respiration produces far more ATP, but risks exposure to oxygen toxicity. ~Anaerobic respiration is less energy-efficient, but allows survival in habitats which lack oxygen. In the human body, both aerobic and anaerobic respiration are important to muscle function

Cell, organelles, and all major metabolic pathways evolved from early prokaryotic cells: List 4 features that are unique to living cells compared with inert chemicals.

~Breath ~Movement ~Respond to stimuli ~Modify itself with the environment

Outline the limitations of using a gram stain and light microscopy to differentiate Bacteria and Archaea

~Convergent Evolution: two pathways (bacterial and archaeal) that arose independently yet lead to similar structure and function. Archaeal cells (w/ pseudopeptidoglycan cell wall) stain gram positive (PURPLE)

Describe how DNA gyrase and topoisomerase act together to regulate chromosome supercoiling.

~DNA gyrase: uses energy from ATP hydrolysis to cut the double helix and introduce negative - right handed - supercoils ~Topoisomerase I: counteracts the gyrase by making single strand breaks and relaxing the negative supercoils and it does it without any ATP energy ~By counteracting each other's activity these 2 topoisomerases ensure that the dsDNA in the nucleoid is overall slightly negative supercoiled; just enough to facilitate strand separation during replication and transcription yet not enough to trigger catastrophic separation of the 2 strands. ~Gyrase & topoisomerase I are regulated by the level of DNA supercoiling ~Too much neg. Supercoiling induces the synthesis of topoisomerase I ~Too little (positive) supercoiling indeed the making of DNA gyrase.

Discriminate b/w enrichment cultures and pure cultures: What is an enrichment culture? How do enrichment cultures favor the growth and survival of a specific microbe of interest over others? What is a pure culture? What are pure cultures used for? What should we know about biochemical testing of a microbe that is combined with other species vs. being alone?

~Enrichment culture= type of growth media favoring the growth and survival of a specific microbe. ~favors the growth and survival of a specific microbe by choosing the nutrients and environmental conditions that will favor that microbe. ~Pure culture= it is a population of cells or multicellular organisms that are growing in the absence of other species. ~they are used for biochemical testing ~when biochemical testing conducted= pure cultures can react way differently in isolation than when combined with other species.

Speculate as to why GFP travels 4 times more slowly in the cytoplasm than in the interior of a mitochondrion (as measured by FRAP).

~FRAP experiments have revealed that fluorescent proteins such as GFP typically diffuse about 10xs more slower in the cytoplasm, and about 4xs more slower in the interior of the mitochondria ~Some large protein complexes do not diffuse through the cytoplasm - instead they concentrate their activities in compartmentalized regions of the cytoplasm. Prokaryotic cells have achieved a workable compromise b/t how much they can accumulate inside the cell and what functions they can carry.

Cells, organelles, and all major metabolic pathways evolved from early prokaryotic cells: Explain why all cells must have a membrane.

~all cells= must have a membrane b/c it is a selectively permeable structure of the cell. ~it allows for movement of selected substances from the outside and inside environment of the cell (200 different kinds of proteins are able to pass through, each of which contains hydrophobic domains to insert themselves into the bilayer) ~The cell membrane anchors the electron transport chin that generates energy for cell growth and function. ~most fundamental role of the cell membrane= provides protection and structure for the cell. ~It allows for all the internal cellular components to stay in their proper location. ~allows for biological molecules to replicate/catalyze reactions in a protected, favorable environment.

Distinguish fermentation from anaerobic respiration.

~Fermentation and anaerobic respiration= happens without O2 ~Instead of ending with glycolysis, like fermentation, anaerobic respiration creates pyruvate through glycolysis, and then creates Acetyl-CoA to generate the TCA cycle and then continues on the same path as aerobic respiration ~Fermentation is essentially the same process. instead of making pyruvate that creates Acetyl-CoA, the final product is a different molecule depending on the type of fermentation. (due to lack of oxygen) In Humans from pyruvate, lactic acid is formed. Long distance runners are familiar with lactic acid. It can build up in the muscles and cause cramping.. Since fermentation does not use the electron transport chain, it is not considered a type of respiration. ~Anaerobic respiration begins the same way as aerobic respiration and fermentation. The first step is still glycolysis and it still creates 2 ATP from one carbohydrate molecule. However, instead of just ending with the product of glycolysis which is pyruvate, it will create Acetyl-CoA, and then continue on the same path as aerobic respiration.

What is the process of fermentation?

~Fermentation is a metabolic process that converts sugar to acids, gases, or alcohol. ~During fermentation, glycolysis converts sugars (glucose) into pyruvate, generating the reduction of NADH via substrate level phosphorylation. ~Fermentative microbes CANT regenerate NAD+ by recycling excess reducing power while making a transmembrane proton gradient and generating ATP → fermentative microbes have evolved other metabolic reactions to dump their excess reducing power.

Describe how adaptions in metabolic pathways allow some bacteria to grow and survive under varying environmental conditions.

~Having these unique adaptations= permits for microbes (like certain types of Bacteria) to thrive in diverse circumstances. ~Looking at facultative aerobic bacteria= they have the ability to change their central metabolism when growing under aerobic or anaerobic conditions. ~Example: E. coli growing aerobically= has the entire TCA cycle, but can replenish oxaloacetate- allowing the cycle to run in reverse. a. By going in reverse, they are able to produce two other precursor metabolites- but lack at generating energy. ~Example: E. coli growing anaerobically= the TCA cycle is operated as two separate arms, working in opposite directions a. one is making precursor metabolites; the other is generating energy

Discriminate b/w anoxygenic and oxygenic photosynthesis

~Here are the main ways that anoxygenic photosynthesis differs from oxygenic photosynthesis: Oxygen is not released because P680 of PSII is not present. ... ~Unlike in oxygenic photosynthesis, where NADPH is the terminal electron acceptor, no NADPH is made because electrons are cycling back into the system.

Bacteria and Archaea exhibit extensive and often unique metabolic diversity (nitrogen fixation, methane production, anoxygenic photosynthesis): Compare and contrast energy harvesting during fueling reactions for heterotrophs and autotrophs.

~Heterotrophs= use organic carbon sources which can also be used to extract electrons and harness energy. ~For this reason, they intertwine their carbon and energy metabolism and simultaneously generate precursor metabolites, ATP, and reducing power. ~Autotrophs= use specific entry and feeder pathways to fix carbon dioxide and make the precursor metabolites in energy consuming reactions. ~Autotrophs have separate fueling reactions to harness energy from the energy source (chemical reactions or light) and drive carbon assimilation.

The survival and growth of any microorganism in a given environment depends on its metabolic characteristics: The broad processes of metabolism (fueling, biosynthesis, polymerization, assembly, and cell division) are interrelated by the fact that each requires starting materials that are the products of the preceding step. Identify the starting products for each phase of metabolism

~Heterotrophy(organic nutrient)/Autotrophy (CO2 + inorganic energy source/light) ~Fueling products: energy (ATP,PMF), precursor metabolites (glucose-6-phosphate and pyruvate), reducing power: NADPH. ~Building blocks: (fatty acids, sugars, amino acids, nucleotides ~lipid, glycogen, protein, dna... ~structures: flagella, pili, cytosol

Cell membranes contain many kinds of proteins (about 70% of the mass of the membrane). Why?

~Membrane proteins perform a variety of functions vital to the survival of organisms: Membrane receptor proteins relay signals between the cell's internal and external environments. Transport proteins move molecules and ions across the membrane. ... Cell adhesion molecules allow cells to identify each other and interact. ~It also needs proteins, which are involved in cross-membrane transport and cell communication, and carbohydrates (sugars and sugar chains), which decorate both the proteins and lipids and help cells recognize each other.

Explain why microbial cells must be stained in order to see them?

~Most prokaryotic cells (microbes) are colorless, so without color they lack sufficient contrast and cant be seen under the microscope. ~Dyes were used to stain the cells and make them clearly visible ~Robert Koch (german microbiologist) discovered the cause of tuberculosis by using differential staining that enabled him to see tubercle bacilli as small dark blue cells within brown stained host tissue. However, the stain procedure has changed over time into differential stains ~Christina Gram developed a differential staining procedure that allowed her to sort bacteria into 2 groups based on the structure of their cell envelope - Gram +/- (purple/red). Knowing the results of the gram stain and the morphology of the infecting bacteria (cocci or bacilli) enables a physician to make a rapid determination of the causative agent and select the most effective ATB treatment.

The structure and function of microorganisms have been revealed by the use of microscopy (including bright-field, phase-contrast, fluorescent, and electron): What is the nucleoid? Identify the consequence of Bacteria and Archaea having their DNA in the cytoplasm rather than in a separate membrane-bounded compartment. What happens once a prokaryotic cell begins to transcribe into a mRNA molecule?

~Nucleoid= it is a region in the cytoplasm prokaryotic cells that contains the genetic material (DNA). It lacks a membrane that is found around the nucleus of eukaryotes. It can contain RNA, proteins, and enzymes that helps with cellular processes. It is used for genome storage (storing DNA or genetic material), transcription, and translation. ~lack of nuclear membrane= offers prokaryotes the opportunity to couple the two essential processes of transcription and translation. ~once a prokaryotic gene begins to be transcribed into a mRNA molecule, ribosomal units latch nascent transcript and translate the information encoded in its sequence to make a protein.

Describe the role of the electron transfer system in respiration.

~Respiration and photosynthesis couple e- transport to p+ pumping to generate the transmembrane ion gradient. ~The electron transfer system/chain (ETS) → a number of membrane bound electron carries hand off the e- (or hydrogens) from one to another down the electrochemical gradient b/t the donor and the acceptor a. In the ETS electron movement is favored by the oxidation-reduction (redox) potentials of components of the chain b. The e- flow through the chain of carrier molecules to a terminal e- acceptor. ~ETS carriers transfer p+ across the membrane in different ways a. Some act as p+ pumps, expelling the p+ at the expense of some the the energy derived from the flow to e- down the energy gradient b. Others pick up protons from the cell interior and release them externally while passing on e- to the next system member, a cytochrome. ~OUTCOME: protons accumulate outside the cell. THis proton shuffle creates a transmembrane p+ gradient, which the ATP synthase can then use to translocate the p+ back to the cytoplasm to energy the phosphorylation of ADP and make ATP. a. If the e- transport stops, p+ pumping and ATP generation would stall, and the cell would stop growing and eventually die.

Identify the benefits of supercoiled chromosomes in Bacteria and Archaea.

~Supercoiling stores energy in the chromosome which is essentially spring loaded ~Supercoiling lowers the energy required to separate the 2 complementary strands of DNA a process needed for both DNA replication and transcription into RNA. ~Prokaryotic cells devote many proteins to keeping it under control - both are topoisomerases (enzymes that change the topology of the DNA). ~Supercoiling helps compact the DNA in the nucleoid. ~Supercoiling also helps with keeping the ends of the DNA safe from exonucleases that would chew up the ends of linear DNA. have DNA that is double helix and twisted, which is grouped up in big loops by anchor proteins ~DNA is negatively charged (anionic) ~Cations in the cell bind to the DNA and neutralize the charge ~DNA binding proteins organize the DNA into supercoils (it is already coiled since it is double-stranded helix)

Microorganisms are ubiquitous and live in diverse and dynamic ecosystems. Discuss how metabolic diversity has allowed microbes to colonize and harness energy from almost any resource on the planet.

~The first phototrophic bacteria to emerge on earth was anoxygenic: they harvested energy from light without generating O2. ~Some bact can shift from anoxygenic photosynthesis to respiring the in the presence of O2. These bact can live in many different environment (dark/light and w/or w/o O2) ~The impact that oxygenic photosynthesis had on the earth and all of its life is immense ~Oxygenic photosynthesis oxygenated the planet and atmosphere a. O2 did kill many microbes existing at the time that cyanobacteria emerged. b. The survivors had evolved detoxification mechanisms to exclude O2 from their cell interior or to keep its concentration v. low ~During respiration e- are transported down the ETS carrieres to the terminal e- acceptor (O2 in this case) while simultaneously pumping p+ across the membrane. This flux creates the transmembrane p+ gradient that the ATP synthase uses to make ATP ~Fermentation makes more sense in anaerobic sediments poor in nitrate and other alternative e- acceptos and also in sediments where competition for these energy sources is high a. Fermentation is a great alternative - it may not generate a lot of ATP but it is enough to get by. b. Fermentative microbes often live in consortia - teams of microbes that cooperate metabolically

State the implications of the hierarchical placing of electron acceptors along the redox tower and the amount of energy harnesses from their respiration.

~The greater the affinity (the higher the molecule appears on the tower) the greater the driving force is on the electron, and the more energy can be harvested

Summarize why hopanoids are important biomarkers for bacteria.

~They are not found in archaea ~They add rigidity and stability to cell membranes ~Unique to certain bacteria ~Indicators of extinct bacteria ~Highly stable at extreme pH and high temps ~Hopanoids help the cell membrane withstand damaging stress conditions, among others high temps, low pH, and detergents.

The structure and function of microorganisms have been revealed by the use of microscopy (including bright-field, phase contrast, fluorescent, and electron). Explain why it is difficult to define what a microbe is? What should we know about the exceptions to microbes, and what is this known as? What should we know about host dependency being extreme? b. List exceptions to the definition that "microbes are free-living organisms so small that they are only visible under the microscope." What is it that viruses lack that makes them not really a microbe? What do viruses have in common with cellular organisms and what is the problem with this? How are they made, and what would happen if they did not have a host cell? What don't viruses have the capacity to make? What do they depend on for this?

~a "microbe" is used to describe a free-living organism so small (usually less then 100 micrometers) that they are only visible under the microscope. ~although many microbes are free-living, there are some exceptions in which the microbe dependent on a host to exist= host dependency ~host dependency can be taken to the extreme, and live inside of the cells of the host. ~Looking at viruses= they can be as big as the smallest bacteria ~not really microbes b/c they lack the key quality of living cells: the capacity to maintain bodily integrity throughout their life cycle. ~reproduce and mutate like cellular organisms, but come apart during their reproductive cycle ~they are made separately and then assembled inside their host cells. W/out the host cell, viruses would not be able to produce progeny viral particles. ~viruses= do not have the capacity to make proteins (they have no ribosomes which are the protein factories of all cells), and rely on the host to supply most, if not all, of the building blocks needed for biosynthesis of their macromolecules.

Discuss how acid fast bacteria can withstand membrane damaging chemicals.

~addition to peptidoglycan, the outer membrane (or envelope) of the acid-fast cell wall contains large amounts of glycolipids (especially mycolic acids). ~it is found in mycobacterium ~mycolic acids= long chains of FA's that create a strong barrier agains the outside world. ~mycolic acid layer= enclosed by a capsule or a slippery structure that is composed of sugars and lipids (this helps to make the cell wall blocked from outside threats.

What are the benefits and drawbacks of using enrichment cultures? What are the benefits and drawbacks of using pure cultures?

~benefits= allows for certain microbes to be detected and identified based on nutritional and environmental needs. ~drawbacks= other fast-growing microbes (referred to as weeds) can flourish in these environments. ~benefits= allows for one to separate and grow a single type of microbe or a single colony of a microbe ~drawbacks=?

Bacteria and Archaea have specialized structures (such as flagella, endospores, and pili) that often confer critical capabilities. Give an example of how structure supports unique function for an intracellular structure: Inclusion bodies? Internal structures? Gas vesicles? Protein shell?

~inclusion bodies= store C and energy resources that the cell can use if nutrients become scarce. ~Internal structures= not organelles b/c they do not contain DNA and maybe never did. ~Gas vesicles= structures that are filled with gas that is similar to the one that dissolves in their cytoplasm. Allows for microbes to have buoyancy, therefore, allowing them to reside close to the surface where light is plentiful, and they can generate energy when needed. (they do not store gas, but they prevent water in the cytoplasm from filtering in) ~Protein shell= they are surrounded by this protein shell which is freely permeable to gasses and also keeps water at bay- any gases that are dissolved in the cytoplasm will diffuse inside the vesicle until its concentration inside the vesicle has reached equilibrium. (maintains the vesicles structure- only when cells are subjected to a sudden increase in hydrostatic pressure do the shells irreversibly collapse)

The survival and growth of any microorganism in a given environment depend on its metabolic characteristics. What does metabolic characteristics allow for microbes to obtain? What factor does the environment play with metabolic characteristics of microbes? What does this allow for determination of that microbe?

~metabolic characteristics= allow for microbes to obtain both nutrients and energy that are needed for survival, growth, and reproduction ~environment= has different chemical and physical properties and allow for a specific microbe to express different metabolic properties. Allows for determination of that microbes ecological niche, making that microbe unique to that specific environment.

5. Although the Central Dogma is universal in all cells, the processes of replication, transcription, and translation differ in Bacteria, Archaea, and eukaryotes: Discuss the differences in general chromosomal structure between Bacteria and Archaea on the one hand and eukaryotes on the other.

~need to answer this! (Look at LO Week 1- google docs )

Compare and contrast the nucleoid of Bacteria and Archaea (prokaryotic organisms) with the nucleus of a eukaryote. Compare and contrast the structure of the cytoplasm in Bacteria and Archaea with that of eukaryotes. ~Look at LO Week 1- google docs for the table of the differences b/w bacteria, archaea, and eukaryote.

~prokaryotes nucleoid= tightly pack a lot of DNA in their nucleoid (supercoiling), and the genome varies considerably. ~the genome has a single chromosome (with some exceptions) ~the genomes chromosome is a circular molecule b/c exonucleases could otherwise chew up the ends of linear DNA molecules (protects them) ~the genome has transcription and translation ~has no true nucleus and DNA is w/in the cytoplasm in the nucleoid ~Eukaryotes nucleus= have a true nucleus (DNA is w/in the membrane bound nucleus) ~DNA is a double helix and does not have supercoiling. prokaryotic cytoplasm: ~gas vesicles change to buoyancy; allow for bacteria to be at correct depth for PS or other light-harvesting activities; protein lets gasses diffuse; exclude water; burst when hydrostatic pressure increases (such as if a bacterial cell falls too deep into the water); common in Cyanobacteria and other aquatic bacteria ~Microcompartments process of photosynthesis and chemosynthesis (needs lots of carbon and chemical energy); phototrophic Cyanobacteria (thylakoids, autotrophic bacteria); carboxysomes (infoldings are used for photosynthesis, harvest light and give off oxygen); inclusion bodies (equip cells to succeed in a particular environment, inclusion bodies aka storage granules, carbon storage when carbon is high and uses inclusion bodies when low in carbon); great source of non-polluting plastics ~Magnetosomes Fe-containing crystals that act like a compass needle; bacteria can orient themselves to a magnetic field such as the magnetic field of the earth ~Prokaryotes (such as bacteria and archaea),- the cytoplasm= is everything that is found inside the plasma membrane. Eukaryotes cytoplasm: ~the cytoplasm is everything b/w the plasma membrane and the nuclear envelope.

Microbes are ubiquitous and live in diverse and dynamic ecosystems. a. Describe three locations where microbes live that are surprising to you.

~they are everywhere and on everything in every environment ~volcanoes= where they have very high and very low temperatures ~deepest parts of the ocean with very high pressure.