Microbiology Exam 2

ETC function within a membrane

The ETC is embedded in a membrane that separates two aqueous compartments -Maintains ion gradient generated by ETC

Regulation of the Calvin Cycle

The expression of the CO2-fixing enzyme varies with CO2 concentration, light levels, and temperature. -CO2 diffuses readily through phospholipid membranes; thus, cells cannot concentrate this substrate across the cell membrane to reach the level needed to drive Rusbisco. The gas concentration problem is solved by: -Conversion of CO2 to bicarbonate ions which is trapped in the cytoplasm, unable to leak out of the cell membrane -Many organisms contain the Rubisco complex within polyhedral structures called carboxysomes -Carboxysome takes up bicarbonate (HCO3-) which is then immediately converted to CO2 by carbonic anhydrase; the CO2 is then fixed by Rubisco

The more solutes in a solution...

The less water available for microbes to use for growth

Water activity

The measure of how much water is available for use

Ecosystem

The non-living place where organisms interact Ex. Ocean, desert, marsh, forest

Oxidative Phosphorylation

The overall process of electron transport and ATP Synthesis

Biosphere

The part of earth where life exists

E. coli K12 and Tephaflex

The polymer is a thermoplastic linear polyester and is produced by means of recombinant fermentation process using E. coli -Easy to grow in controlled environment -If it leaks into environment, it dies -Safe -No toxins or plasmids

Microbial ecology

The study of relationships of microorganisms to each other and their environment

Generation Time

The time is takes for a population to double

How did they fix the problem of slow growing Pseudomonas putida CBB5?

They transferred the caffeine gene/operon into E. coli to create caffeine addicted E. coli

Too small of windrow

They will not heat up properly

Temperature phases

Three phases: 1. Mesophilic 2. Thermophilic 3. Mesophilic

How are TCA Cycle and glucose catabolism connected?

Through pyruvate breakdown to Acetyl-CoA which enters the TCA Cycle by condensing with 4-oxaloacetate to form citrate

How do halophiles deal with high salt concentration?

To achieve a low internal concentration of Na+, halophilic microbes use special ions pumps to excrete sodium and replace it with other cations, such as K+

What do cells need energy for?

To move and grow

Tolerance to environmental habitat is based on...

Tolerance of macromolecules

Particle size: too big and too small

Too big: Not enough surface area so decomposition takes forever; lowers C:N ratio Too small: Compacts tightly and creates anaerobic environment

Water: too wet and too dry

Too wet: Water will fill the pore space needed to for air movement, and anaerobic conditions can result Too dry: The decomposition rate will slow down

Energy flow in an ecosystem

Transfer of energy causes a loss of energy as heat (90% lost) Ex. Warm, murky pond

True or False. Many prokaryotes use more than one of the types of metabolism.

True

True or false. Sporulation is highly regulated and stochastic.

True. Stochastic = randomly determined

Alkaliphiles and Sodium Motive Force

Use Na+ motive force in addition to PMF to do much of the work of the cell -Rely heavily on Na+/H+ antiporters to bring in protons (keep pH lower) -Sodium gradient powers flagellar rotation and transport nutrient solutes (PMF still needed for ATP synthase)

Heterotrophs

Use performed organic molecules (external sources of organic carbon compounds)

Fermentation and final electron acceptor

Uses organic molecules as a final electron acceptor (Ethanol and lactic acid)

Water and life

Water is critical to life -All microorganisms require water for growth

Acid and the bacterial cell

Weak acids can pass through membranes when uncharged -Dissociate intracellularly and disrupt the cell pH homeostasis, has direct effect on macromolecular structures, and thus prevents cell growth -Used to preserve foods

Biomass

Weight of all organisms present

Halotolerant

Withstand up to 10% salt concentration

Can an extremophile be extreme in multiple conditions?

Yes, those that live by thermovents are extreme in temperature and pressure.

Which of the following forms of energy production does NOT involve the formation of a proton gradient to synthesize ATP? Select one: a. Fermentation b. Oxidative respiration c. Phototrophy d. All forms of energy production require a proton motive force.

a. Fermentation During fermentation, redox reactions happen in the cytoplasm and ATP is generated via substrate-level phosphorylation. Both oxidative respiration and phototrophy use electron transport systems to create ion gradients. For more information, see Section 14.2.

Which of the following is an example of catabolism? Select one: a. Glucose oxidation to pyruvate b. Starch production from glucose c. Lipid synthesis from fatty acids and glycerol d. Amino acid polymerization into proteins

a. Glucose oxidation to pyruvate Catabolism is the breakdown of a molecule into smaller molecules, which often releases energy. Of the choices listed, only glucose oxidation into two molecules of pyruvate is catabolic. The other choices are examples of anabolic reactions. For more information, see Section 13.4.

In a bacterial cell, which of the following pathways take place in the cytosol? Select one or more: a. Glycolysis b. Lactic Acid Fermentation c. Ethanol Fermentation d. TCA cycle e. Pentose-phosphate pathway

a. Glycolysis b. Lactic Acid Fermentation c. Ethanol Fermentation d. TCA cycle e. Pentose-phosphate pathway

Which of the following sentences is true? Select one: a. If a bacterium's cell volume decreases after it is placed in solution A, then solution A is hypertonic relative to the bacterium. b. If a bacterium's cell volume decreases after it is placed in solution A, then solution A is hypotonic relative to the bacterium. c. If a bacterium's cell volume decreases after it is placed in solution A, then solution A is isotonic relative to the bacterium. d. If a bacterium's cell volume decreases after it is placed in solution A, then solution A is thermotonic relative to the bacterium.

a. If a bacterium's cell volume decreases after it is placed in solution A, then solution A is hypertonic relative to the bacterium. In a hypertonic solution, water will flow out of the bacteria by osmosis. This will decrease cell volume. In a hypotonic solution, water will flow into a bacterium by osmosis. In an isotonic solution, the bacterium is at water equilibrium with its environment. For more information, see Section 5.4.

Which of the following is NOT true of proton motive force in bacteria? Select one: a. It is used in the generation of energy in the form of ADP. b. It is used to turn the flagellar motor. c. It can be used for nutrient transport. d. It produces a transmembrane electrochemical gradient. e. All of the options are true

a. It is used in the generation of energy in the form of ADP.

All of the following are true about microbes and temperature EXCEPT: Select one: a. Microbes have mechanisms to control their temperature. b. Temperature affects the average rate of molecular motion. c. Changes in temperature affect membrane fluidity. d. Changes in temperature affect transport. e. Every organism has an optimum temperature for growth.

a. Microbes have mechanisms to control their temperature.

Most extremophilic organisms are Select one: a. archaea. b. bacteria. c. eukaryotes. d. plants.

a. archaea. Archaea have been found in the most extreme (by human standards) conditions. Eukaryotes, such as plants, are least able to tolerate extreme conditions. For more information, see Section 5.2.

Some bacteria form environmentally resistant forms called: Select one: a. endospores b. heterocysts c. colonies d. hyphae e. actinomycetes

a. endospores

The time interval required for the formation of two cells from one is called the: Select one: a. generation time b. growth time c. growth rate d. exponential rate e. log phase

a. generation time

Organisms that need to ingest reduced carbon are called Select one: a. heterotrophs. b. autotrophs. c. lithotrophs. d. phototrophs.

a. heterotrophs. While autotrophs are self-feeding (meaning they assimilate CO2 as a carbon source, reducing it to make cell constituents), heterotrophs need to ingest reduced carbon. Lithotrophs generate ATP from reduced inorganic compounds and phototrophs generate ATP via light. Lithotrophs and phototrophs may be either autotrophs or heterotrophs. For more information, see Section 4.1.

A __________ medium is one of higher osmolarity (higher solute) than the cell. Select one: a. hypertonic b. hypotonic c. isotonic d. defined e. complex

a. hypertonic

In Gram-negative bacteria, the ETS is embedded in the: Select one: a. inner membrane b. cell wall c. periplasm d. outer membrane e. none of the above

a. inner membrane

Fermentation pathways have in common the Select one: a. oxidation of NADH to NAD+. b. production of lactic acid. c. production of ethanol. d. use of oxygen as an electron acceptor.

a. oxidation of NADH to NAD+. All fermentation pathways regenerate NAD+ for use in glycolysis. Fermentation uses an organic compound, such as pyruvate, as an electron acceptor. The specific products differ depending on the fermentation pathway. For more information, see Section 13.6.

Enzymes transferring electrons at the start of the ETS are referred to as __________, whereas enzymes transferring electrons to the terminal electron acceptor are designated as __________. Select one: a. oxidoreductases (dehydrogenases); terminal oxidases b. terminal oxidases; oxidoreductases (dehydrogenases) c. sulfatases; nitrogenases d. oxidoreductases (dehydrogenases), ATP synthases e. terminal oxidases, ATP synthases

a. oxidoreductases (dehydrogenases); terminal oxidases

During biofilm formation, as more and more cells bind to the surface, they begin sending signals to each other in a process called: Select one: a. quorum sensing b. homoserine lactone sensing c. siderophores iron acquisition d. polysaccharides uptake e. density sensing

a. quorum sensing

Organisms that must use oxygen as a final electron acceptor in electron transport chains are Select one: a. strict aerobes. b. aerobes. c. anaerobes. d. strict anaerobes.

a. strict aerobes. Strict aerobes can only use oxygen as a final electron acceptor in their electron transport chains. Although aerobes can grow in the presence of oxygen, they do not necessarily use oxygen as the final electron acceptor in the electron transport chain. Anaerobes do not use oxygen and strict anaerobes are killed by oxygen. For more information, see Section 5.6.

In which case would the shortest lag period most likely be observed? Select one: a. transfer from complex medium to fresh complex medium b. transfer from complex medium to minimal medium c. transfer to a lower temperature d. transfer to a different pH e. transfer to a different salt concentration

a. transfer from complex medium to fresh complex medium

When dimolecular oxygen serves as the electron acceptor at the end of an electron transport chain, the product is Select one: a. water. b. NADH. c. carbon dioxide. d. a hydrogen ion.

a. water. Oxygen gas accepts electrons and protons to form water. For more information, see Section 14.1

A cafeteria worker who fails to wash his hands thoroughly and fails to wear gloves inoculates a quiche with four E. coli cells when he uses his finger to test whether it is done. By the time you purchase the quiche, there are 128 E. coli cells in it. How many generations did the cells go through? Select one: a. 4 b. 5 c. 8 d. 32 e. 64

b. 5

After completion of a turn of the tricarboxylic acid (TCA) cycle, most of the energy originally present in glucose is now found in Select one: a. ATP. b. NADH. c. carbon dioxide. d. pyruvate.

b. NADH. At the end of one turn of the TCA cycle only four ATPs have been produced. During the TCA cycle the carbons in the acetyl group of acetyl-CoA become oxidized and NADH is produced. NADH will release its energy to form ATP through electron transport systems. Carbon dioxide is a low-energy waste product. Pyruvate is the end product of EMP and Entner-Doudoroff pathways. For more information, see Section 13.6.

Most enzymes are which type of biomolecule? Select one: a. Lipids b. Proteins c. RNA d. Sugars

b. Proteins Most enzymes are proteins. Some enzymes in which RNA is responsible for catalysis are called ribozymes. Lipids and sugars have not been found to perform catalytic activities. For more information, see Section 13.3.

__________ are prominent flora beneath icebergs in the Arctic and Antarctic. Select one: a. Barophiles b. Psychrophiles c. Mesophiles d. Thermophiles e. Acidophiles

b. Psychrophiles

Which of the following is NOT true about thermophiles? Select one: a. Their proteins contain less glycine. b. They have more unsaturated linear lipids in their membranes. c. They have chaperone proteins. d. Their genomes are packed with numerous DNA-binding proteins that stabilize DNA. e. They have a higher GC content in DNA

b. They have more unsaturated linear lipids in their membranes.

Which of the following are NOT pathways that convert NADH into NAD+? Select one or more: a. Ethanol fermentation b. Tricarboxylic acid cycle c. Glycolysis d. Pentose-phosphate pathway e. Lactic Acid Fermentation

b. Tricarboxylic acid cycle c. Glycolysis d. Pentose-phosphate pathway

How many phosphate groups does ADP contain? Select one: a. One b. Two c. Three d. None

b. Two ADP stands for adenosine diphosphate, the "di" prefix indicates that two phosphates are present. For more information, see Section 13.3.

Some organisms can create a sodium motive force by pumping sodium ions across a membrane using the energy of an electron transport system. In order for this sodium motive force to provide useful energy for the cell, the organism must contain Select one: a. a H+-driven ATP synthase. b. a Na+-driven ATP synthase. c. bacteriorhodopsin. d. a sodium oxidase enzyme complex.

b. a Na+-driven ATP synthase. If sodium ions are pumped to one side of the membrane creating a sodium motive force, then potential energy created can be used to create ATP with an Na+-driven ATP synthase in an analogous manner as proton motive forces are formed from pumping H+. For more information, see Section 14.3.

The Calvin cycle is essentially: Select one: a. started by the oxygen capture by Rubisco b. a reductive pentose phosphate cycle c. the reductive, or reverse, tricarboxylic acid cycle d. all of the above e. none of the above

b. a reductive pentose phosphate cycle

Growth of most microorganisms occurs by: Select one: a. budding b. binary fission c. replication d. conjugation e. transformation

b. binary fission

Photoheterotrophic organisms Select one: a. can subsist solely on light and inorganic substrates. b. can use light as an energy source, but must still acquire reduced carbon from the environment. c. can use light to fix carbon dioxide, but must acquire reduced compounds from the environment as electron donors to power ATP synthesis. d. only existed on early Earth and are now all extinct.

b. can use light as an energy source, but must still acquire reduced carbon from the environment. The prefix "photo" implies that the organism can make ATP from light energy and the term "heterotroph" indicates that the organism must acquire reduced carbon from the environment for biosynthetic purposes. While photoheterotrophy is an ancient metabolic strategy, there are organisms alive today that are photoheterotrophs. For more information, see Section 14.6.

Some bacteria live in deep sea vents where no light penetrates, yet are still capable of producing their own reduced carbon. These organisms are classified as Select one: a. photoheterotrophs. b. chemoautotrophs. c. chemoheterotrophs. d. photoautotrophs.

b. chemoautotrophs. Chemoautotrophs produce energy from oxidizing inorganic molecules (hence the chemo part of the name) and can use some of this energy to reduce CO2 (hence the auto part of the name). For more information, see Section 4.1.

During which stage of bacterial growth is the culture growing exponentially? Select one: a. lag b. early log c. late log d. stationary e. death

b. early log

What type of growth pattern is represented here: 5 × 103; 1 × 104; 2 × 104; 4 × 104; 8 × 104? Select one: a. linear b. exponential c. lag d. generation e. semilogarithmic

b. exponential

Compared with eukaryotic electron transport chains, the transport chains of Escherichia coli Select one: a. create a proton motive force. b. have a wider diversity of alternative oxidoreductases (dehydrogenases) and terminal oxidases. c. are located in a membrane. d. generate energy that can power an ATP synthase.

b. have a wider diversity of alternative oxidoreductases (dehydrogenases) and terminal oxidases. A wider diversity of dehydrogenases and oxidases allows E. coli to use a variety of molecules, depending on environmental conditions. In both eukaryotes and prokaryotes, electron transport systems are located in a membrane. For more information, see Section 14.3.

By themselves, heterotrophs would deplete the world of __________ sources and starve to death. Select one: a. usable nitrogen b. organic carbon c. water d. energy e. oxygen

b. organic carbon

Cyanobacteria are an example of Select one: a. photoheterotrophs. b. photoautotrophs. c. chemoheterotrophs. d. chemoautotrophs.

b. photoautotrophs. Cyanobacteria can use light (photo) to create ATP and can reduce CO2 into sugar, so they are photoautotrophs. For more information, see Section 4.1.

Alkaliphiles use _________________ in addition to proton motive force to maintain pH. Select one: a. potassium motive force b. sodium motive force c. calcium motive force d. magnesium motive force e. sulfur motive force

b. sodium motive force

Electron transport systems in bacteria and archaea are embedded in what membrane systems? Select one or more: a. mitochondrial inner membrane b. thylakoids c. the inner membrane of Gram-negative bacteria d. the cytoplasmic membrane of Gram-positive bacteria e. chloroplasts

b. thylakoids c. the inner membrane of Gram-negative bacteria d. the cytoplasmic membrane of Gram-positive bacteria

Psychrophiles favor the cold since their membranes are more fluid at low temperature as a result of the high proportion of __________ present. Select one: a. saturated fatty acids b. unsaturated fatty acids c. lipopolysaccharides d. transport proteins e. water

b. unsaturated fatty acids

If a bacterium can divide once an hour, after 5 hours, 1 bacterium will yield Select one: a. 5 bacteria. b. 10 bacteria. c. 32 bacteria. d. 50 bacteria.

c. 32 bacteria. The number of organisms after n generations will be N0 (the initial number of bacteria. x 2n. Since we are told the generation time is 1 hour, 5 hours yields five generations. 1 x 25 = 32. For more information, see Section 4.5.

If an organism produces seven offspring per generation, which of the following would express the rate of increase in population, where n corresponds to the number of generations? Select one: a. 2^n b. n^2 c. 7^n d. n^7 e. 2n^7

c. 7^n

The products of oxygenic photosynthesis include Select one: a. ATP, NADP+, and water. b. ATP, NADPH + H+, and quinone. c. ATP, NADPH + H+, and O2. d. ATP, NADP+, and chlorophyll.

c. ATP, NADPH + H+, and O2. Oxygenic photosynthesis uses light energy to strip electrons from water forming O2. The stripped electrons pass through an electron transport chain and ultimately result in the formation of ATP and NADPH. For more information, see Section 14.6.

__________ are responsible for the carbon-fixation component of the carbon cycle. Select one: a. Heterotrophs b. Symbionts c. Autotrophs d. Chemotrophs e. Organotrophs

c. Autotrophs

Which of the following is true of cells in batch culture? Select one: a. Cells never reach exponential growth rates. b. Metabolic wastes do not accumulate. c. Cells will not remain at a constant mass. d. New batches of media are added during culture.

c. Cells will not remain at a constant mass. During batch culturing, no new media are added. As nutrients are depleted and metabolic wastes accumulate, cell size may be reduced and the cells will enter a stationary phase. For more information, see Section 4.5.

Which of the following is true of endospores? Select one: a. All bacterial species can produce endospores. b. Endospores are produced from vegetative cells when nutrients are abundant. c. Endospores are resistant to many stresses that would kill vegetative cells. d. Endospores can only germinate into viable vegetative cells within 10 years.

c. Endospores are resistant to many stresses that would kill vegetative cells. An endospore is a durable, heat-resistant spore that can remain viable for thousands of years. Only some Gram-positive bacteria are capable of endospore formation, often in response to nutrient limitation. For more information, see Section 4.7.

Electron transport chains pump which of the following across membranes? Select one: a. Molecules b. Atoms c. Ions d. Neutrons

c. Ions Electron transport chains transfer electrons from one carrier to the next, but ions (such as protons, not hydrogen atoms) are pumped across the membrane. For more information, see Section 14.1.

The tricarboxylic acid (TCA) cycle is also known as the Select one: a. Pentose Phosphate Pathway. b. Glycolysis. c. Krebs cycle. d. Calvin cycle.

c. Krebs cycle. Hans Krebs played a pivotal role in determining the TCA cycle, and shared a Nobel Prize for this work. The EMP pathway is another name for glycolysis. Some bacteria use the Entner-Doudornoff pathway as an alternative to EMP for glucose oxidation to pyruvate. The Calvin cycle is involved in carbon dioxide fixation. For more information, see Section 13.6.

This molecule CANNOT freely cross biological membranes: Select one: a. O2 b. CO2 c. NH4+ d. all choices can freely cross e. H2

c. NH4+

Bacteria synthesize ribose for nucleotides using which pathway? Select one: a. Glycolysis b. Lactic Acid Fermentation c. Pentose phosphate pathway d. Tricarboxylic acid cycle e. All of the options

c. Pentose phosphate pathway

__________ enzymes are stable in part because they contain relatively low amounts of the amino acid glycine. Select one: a. Psychrophilic b. Acidophilic c. Thermophilic d. Halophilic e. Barophilic Feedback

c. Thermophilic

Is it possible to produce a proton motive force without an electron transport system? Select one: a. Yes, by making a cell membrane permeable to protons. b. Yes, by using an ion other than H+. c. Yes, by using a membrane-bound protein pigment capable of behaving as a proton pump. d. No, it is not possible.

c. Yes, by using a membrane-bound protein pigment capable of behaving as a proton pump. Some microorganisms containing bacteriorhodopsin use light to pump protons. If a membrane is made permeable to protons, the gradient dissipates and uncoupling results. Although other ions, such as sodium, may form transmembrane gradients, the question alludes exclusively to protons. For more information, see Section 14.6.

An organism that grows best at high osmolarity (higher solute) is called Select one: a. an alkaliphile. b. a psychrophile. c. a halophile. d. a barophile.

c. a halophile. Halophiles thrive in high-solute environments. Alkaliphiles grow best in high pH, psychrophiles grow best in cold environments, and barophiles grow under high-pressure conditions. For more information, see Section 5.1.

A bacterial pathogen that can cause septicemia (infection of the blood) is likely Select one: a. an acidophile. b. an alkaliphile. c. a neutralophile. d. a hemophile.

c. a neutralophile. The blood has nearly a neutral pH, so any organism growing here is a neutralophile. For more information, see Section 5.5.

Many alkaliphiles have Select one: a. intracellular proteins that can withstand a pH of 2. b. intracellular proteins that can withstand a pH of 12. c. a sodium motive force. d. triple-stranded DNA as their genetic material.

c. a sodium motive force. Because it will be hard to maintain a proton motive force in an alkaline environment, many alkaliphiles use a sodium motive force as a source of potential energy. Even though alkaliphiles live in alkaline environments, internal proteins do not function well above a pH of 8. For more information, see Section 5.5.

When the population doubles during each given unit of time, the growth is: Select one: a. linear b. semilogarithmic c. exponential d. geometric e. arithmetic

c. exponential

A microbial population explosion results from the sudden availability of: Select one: a. water b. oxygen c. food d. sunlight e. prey

c. food

Metabolism using an electron transport system is classified based on the nature of the initial electron donors and terminal electron acceptors. Lithotrophy uses Select one: a. organic molecules as the initial electron donors. b. organic molecules as the terminal electron acceptors. c. inorganic molecules as the initial electron donors. d. inorganic molecules as the terminal electron acceptors.

c. inorganic molecules as the initial electron donors. Lithotrophy (also known as chemolithotrophy) uses inorganic molecules as the initial electron donors. The electron acceptors may be organic or inorganic. For more information, see Section 14.1 and 14.5.

The correct order of phases for bacteria inoculated into a new culture medium is Select one: a. stationary, log, lag, death. b. log, lag, stationary, death. c. lag, log, stationary, death. d. lag, stationary, log, death.

c. lag, log, stationary, death. When bacteria are placed into a new culture medium there is a lag before logarithmic growth. As nutrients run out, the culture enters a stationary phase, finally followed by death. For more information, see Section 4.5.

Quorum sensing begins during which growth stage? Select one: a. lag b. early log c. late log d. stationary e. death

c. late log

The proteins of the electron transport systems are usually Select one: a. located in the cytoplasm. b. associated with DNA. c. located within a membrane. d. None of the options are correct

c. located within a membrane. The proteins of the electron transport chain are associated with membranes, where they can produce a transmembrane ion gradient. For more information, see Section 14.1.

Human pathogens are: Select one: a. halophiles b. psychrophiles c. mesophiles d. thermophiles e. extreme thermophiles

c. mesophiles

One reason most organisms cannot grow at high temperatures is that Select one: a. membranes will stiffen. b. diffusion rates slow down. c. proteins denature. d. DNA base pairs become too stable.

c. proteins denature. At high temperatures, noncovalent bonds responsible for protein secondary and tertiary structure will break leading to protein denaturation. Other changes at high temperatures are increased membrane fluidity and increased diffusion rates. For more information, see Section 5.2.

Which of the following is NOT an end product of fermentation? Select one: a. carbon dioxide b. acetone c. pyruvate d. butanol e. none of the above

c. pyruvate

The proton motive force is a source of energy that can directly power all of the following EXCEPT the Select one: a. production of ATP. b. rotation of bacterial flagella. c. synthesis of proteins from amino acids. d. import of other ions against their concentration gradients.

c. synthesis of proteins from amino acids. Ribosomes do not use the proton motive force for protein synthesis. The proton motive force can be used to drive secondary active transport, to produce ATP via ATP synthase, and to rotate bacterial flagella. For more information, see Section 14.2.

The greatest amount of reduced coenzyme NADH + H+ is produced during which stage of aerobic respiration? Select one: a. glycolysis b. pyruvate conversion to acetyl-CoA (ie the "bridge step) c. tricarboxylic acid cycle d. ethanol fermentation e. pentose phosphate pathway

c. tricarboxylic acid cycle

Which of the following is a possible substrate for catabolism? Select one: a. Amino acid b. Lipid c. Sugar d. All of the above

d. All of the above Cells can catabolize many different types of substrates. For more information, see Section 13.4. Feedback

Which of the following is correct regarding fermentation? Select one: a. It consists of partial breakdown of organic molecules without an electron transport system. b. In fermentative reactions, electrons from organic substrates are put back onto organic products. c. It occurs in the absence of oxygen. d. All of the options are correct e. None of the options are correct

d. All of the options are correct

Which of the following molecules can serve as an electron donor to fuel an electron transport chain? Select one: a. NADH b. Water c. Ammonia d. All of the options are correct

d. All of the options are correct Many different reduced molecules can serve as electron donors at the start of electron transport chains. For more information, see Section 14.1.

Many microbes can use alternative terminal electron acceptors such as Select one: a. Nitrate (NO3-) b. Sulfate (SO4-) c. Fumarate (-O2C-CH=CH-CO2-) d. All of the options are correct

d. All of the options are correct Bacteria such as Desulfovibrio can use nitrate and sulfate as electron acceptors. Some chemoorganotrophs can use organic electron acceptors such as fumarate. For more information, see Section 14.5.

NADH is an Select one: a. electron donor. b. electron acceptor. c. energy carrier. d. Both a and c

d. Both a and c NADH is an electron donor and also an energy carrier. For more information, see Section 13.3.

In oxygenic photosynthesis, __________ is the electron donor, whereas in anaerobic photosynthesis it can be succinate or __________. Select one: a. H2S; S0 b. O2; H2 c. O2; H2O d. H2O; H2S e. all of the above

d. H2O; H2S

Which metabolic pathway has ribulose-5-phosphate as an intermediary? Select one: a. Ethanol Fermentation b. Tricarboxylic acid cycle c. Glycolysis d. Pentose-Phosphate Shunt

d. Pentose-Phosphate Shunt Ribulose-5-phosphate is an intermediary in the pentose-phosphate shunt (aka pentose phosphate pathway). For more information, see Section 13.5.

Polysaccharides are polymers of which monomer? Select one: a. Amino acids b. Deoxyribonucleotides c. Fatty acids d. Sugars

d. Sugars Sugars (also known as monosaccharides) can polymerize into polysaccharides. Amino acids polymerize to form proteins, deoxyribonucleotides polymerize to form DNA, and fatty acids can help form certain types of lipids. For more information, see Section 13.4.

Which of the following is true of all biofilms? Select one: a. They only contain a single species. b. The EPS may be protein or polysaccharide. c. Cells in the biofilm are dormant until the bacteria leave the biofilm. d. The EPS is secreted by the bacteria. e. It is a continuous monolayer surface deposit.

d. The EPS is secreted by the bacteria.

Which best describes microaerophiles? Select one: a. They require atmospheric oxygen levels to grow. b. They cannot grow in the presence of oxygen. c. They will use oxygen if it is present, but can grow even if oxygen is not present. d. They require a small amount of oxygen. e. They can't use oxygen to grow, but oxygen won't kill them.

d. They require a small amount of oxygen.

A bacterium that thrives in your stomach is probably a/an: Select one: a. thermophile b. neutrophile c. alkaliphile d. acidophile e. psychrophile

d. acidophile

The proton motive force drives the following process in bacteria: Select one: a. ATP biosynthesis from ADP and Pi b. flagellar rotation c. nutrient uptake d. all of the above e. none of the above

d. all of the above

Scientists study microbial growth because Select one: a. learning what makes bacteria grow can lead to insights on how to prevent their growth. b. many microbes are used for commercial, industrial purposes. c. microbes can serve as model organisms for fundamental biological processes. d. all of the above

d. all of the above Scientists study microbial growth for many different reasons and seek answers to clinical, industrial, and basic biological questions. For more information, see Section 4.5.

Proteins have optima for Select one: a. temperature. b. pH. c. osmolarity. d. all options are correct

d. all options are correct A protein works best at a particular temperature, pH, and osmolarity. Different proteins may have different optima for these variables. For more information, see Section 5.1.

Many __________ have been isolated from the ocean floor environment. Select one: a. psychrophiles b. mesophiles c. thermophiles d. barophiles e. acidophiles

d. barophiles

An organism contains photosystem II but not photosystem I. From this you can conclude that the organism Select one: a. uses water as an electron donor, liberating oxygen gas. b. can produce both NADPH and ATP from light energy. c. can produce NADPH from light energy, but not ATP. d. can produce ATP from light energy, but not NADPH.

d. can produce ATP from light energy, but not NADPH. Electron flow from photosystem II is associated with ATP production; in photosystem I, electrons are used to produce NADPH. For more information, see Section 14.6.

Barophilic bacteria and archaea are found primarily Select one: a. on cold mountains. b. in environments enriched in the element barium. c. in the human gastrointestinal tract. d. deep in the ocean.

d. deep in the ocean. Barophilic organisms prefer high-pressure environments, such as can be found at great ocean depths. For more information, see Section 5.3.

Many barophiles are also psychrophilic because Select one: a. it is cold at the high, mountain top elevations where barophiles grow. b. it is difficult for enzymes to function at high pressure and above 20ºC. c. it is usually warm at the ocean depths. d. it is usually cold at the ocean depths.

d. it is usually cold at the ocean depths. Barophiles, which require high pressures to grow, can be found in ocean depths. Since the average temperature at the ocean's floor is 2ºC, many barophiles are also psychrophiles. There is no evidence that it is difficult for enzymes to function at high pressure and above 20ºC as barophilic hyperthermophiles form the basis of thermal vent communities. For more information, see Section 5.3.

Biofilms Select one: a. are flat, two-dimensional films of bacteria. b. contain only a single species of bacteria. c. are relatively rare. d. may cause health problems for humans.

d. may cause health problems for humans. Biofilms are three-dimensional assemblages of bacteria that may contain multiple species. Biofilms are common in nature. Biofilm colonization of medical instruments may lead to infections. For more information, see Section 4.6.

A continuous culture differs from a batch culture because in continuous culture, Select one: a. the temperature is held constant. b. the flask is continuously shaken. c. the temperature continuously increases. d. new media is added and old media removed.

d. new media is added and old media removed. In contrast to the closed-system batch culture, in continuous culture new media is added and old media removed. This allows bacteria to remain in a log phase for extended periods, facilitating analysis of microbial physiology. Differences in temperature and/or shaking do not discriminate between batch and continuous culture. For more information, see Section 4.5.

What is lithotrophy? Select one: a. breakdown of molecules using light energy b. oxidation of organic electron donors to CO2 and H2O c. photolysis of H2S or H2O coupled to CO2 fixation d. oxidation of inorganic electron donors such as Fe2+ using O2 or anaerobic electronic acceptors e. none of the above

d. oxidation of inorganic electron donors such as Fe2+ using O2 or anaerobic electronic acceptors

The fastest growth rate for a species occurs at temperatures where a cell's __________ work most efficiently. Select one: a. lipids b. membranes c. nucleic acids d. proteins e. polysaccharides

d. proteins

Aerobes may tolerate the presence of oxygen because they have the enzyme Select one: a. DNA gyrase. b. RNA polymerase. c. NADH dehydrogenase II. d. superoxide dismutase.

d. superoxide dismutase. Superoxide dismutase removes reactive dangerous oxygen species. The other enzymes listed do not remove reactive oxygen species. In fact, NADH dehydrogenase II can catalyze the formation of reactive oxygen species. For more information, see Section 5.6.

A particular organism converts Fe2+ to Fe3+ during anaerobic respiration. In this case, Select one or more: a. Fe3+ is an electron donor. b. Fe3+ is an electron acceptor. c. Fe2+ is an electron acceptor. d. None of the options are correct e. Fe2+ is an electron donor. f. Oxidoreductase is an electron acceptor g. Oxidoreductase is an electron donor

e. Fe2+ is an electron donor. f. Oxidoreductase is an electron acceptor

__________ grow at temperatures as high as 121°C, which also occur under extreme pressure. Select one: a. Thermophiles b. Extreme halophiles c. Psychrophiles d. Hyperpsychrophiles e. Hyperthermophiles

e. Hyperthermophiles

A problem with __________ of cell number is that dead cells also scatter light. Select one: a. direct microscopic counts b. viable counts c. spread plate counts d. pour plate counts e. optical density measurements

e. optical density measurements

Acidophiles range

pH 0-5

Neutralophiles range

pH 5-8 -Most pathogens and microbes

Alkaliphiles range

pH 9-11

Batch culture

-A liquid medium in a closed system -Allows us to calculate generation time and how changing conditions affect bacterial physiology and growth

How do cells deal with reactive oxygen species?

-Almost all organisms growing in the presence of oxygen produce the enzyme superoxide dismutase (SOD) -Almost all produce catalase

Biosynthesis in autotrophs

-Anabolism -The building of complex biomolecules

Who is living and working in the compost?

-Bacteria are primary consumers and decomposers -Invertebrates

Optimal composting conditions: -Carbon:Nitrogen -Oxygen -Water -pH -Temperature

-Carbon:Nitrogen = 30:1 -Oxygen = >10% -Water = 40-60% moisture -pH = 5.5-8.5 -Temperature = 90-140F

Rubisco

-Catalyzes the condensation of CO2 and R-5-P and the splitting of the unstable 6C intermediate into two 3C PGA molecules

Pseudomonas putida CBB5

-Discovered in soil of flower bed -Can live on caffeine as a sole carbon and nitrogen source by metabolizing caffeine to xanthine to make RNA/DNA and ammonia and CO2 BUT GROWS VERY SLOWLY

What limits a cell's growth at high temperatures?

-Enzymes can be unfolded at high temperatures; proteins are denatured -Membrane lipids "melt" -DNA denaturation

Requirements of biosynthesis

-Essential elements: C, H, O, N -Reduction: By reducing agents such as NADPH -Energy: By coupling reactions to ATP hydrolysis, NADPH oxidation, or ion glow down transmembrane concentration gradient

Entner-Douderoff Pathway

-Evolved earlier than EMP -Used by gut bacteria -Still get pyruvate.

Which pathways in heterotrophic metabolism do not produce ATP?

-Fermentation -PDC/Bridge step

Properties of Tephaflex

-Flexible -Strong (high tensile strength) -The body quickly metabolizes it

Name three different ways ATP can be generated.

-GLYCOLYSIS Glycolysis is one method of producing ATP and occurs in almost all cells. This process is an anaerobic catabolism of glucose that converts a molecule of glucose into two molecules of pyruvic acid and two molecules of ATP. -OXIDATIVE PHOSPHORYLATION Oxidative phosphorylation also produces ATP and is a major producer of ATP in organisms -- 26 out of 30 molecules of ATP generated from glucose are produced through oxidative phosphorylation. In oxidative phosphorylation, ATP is produced when electrons flow from chemicals known as NADH or FADH (nicotinamide adenine dinucleotide and flavin adenine dinucleotide respectively) to oxygen. AEROBIC RESPIRATION Aerobic respiration is the final way that ATP is formed. Aerobic respiration also uses glucose to produce ATP and as the name indicates, oxygen must be present for the process to occur. Without oxygen, aerobic respiration converts to anaerobic respiration, which only produces 2 ATP compared to aerobic respirations 34. Anaerobic respiration results in lactate build up in animals, or alcohol and carbon dioxide build up in yeast and plants.

How are microbes classified based on osmolarity?

-Halotolerant -Halophiles

Continuous culture

-In a continuous culture, all cells in a population achieve a steady state, which allows detailed study of bacterial physiology -The chemostate ensures logarithmic growth by constantly adding and removing equal amounts of culture media

Caffeine and rivers

-In our bodies, caffeine has a half-life of 1-2 hours; however, we excrete it in our urine before caffeine is destroyed. -Caffeine is brought to the rivers and has a half life of 12 days in the rivers. -The buildup of caffeine in rivers kills many organisms that live there.

Fermentation Pathways

-Lactic acid -Ethanol

Phases of bacterial growth curve

-Lag -Log/Exponential -Stationary -Death

Hypotonic solution

-Less solutes outside the cell -Water rushes in -Causes osmolysis

Municipal Solid Waste vs Compost

-MSW is almost entirely anaerobic -MSW has much larger C:N ratio (150:1) -A lot of toxic by-products are washed into the stream

What temperature group is most likely to include human pathogens and how does this information relate to food preservation?

-Mesophiles are more likely to include human pathogens -We preserve food in cold temperatures below the mesophile optimal growth temperatures to limit their growth

Hypertonic solution

-More solutes outside the cell -Water rushes out -Causes plasmolysis

Environmental Impact of Caffeine

-Most organisms cannot efficiently degrade caffeine -Significant accumulation in the environment for industrial and waste water sources -Caffeine levels are used to measure impact on bodies of water --> May signal other signs of pollution (pesticides, pharmaceuticals, etc)

What is the preferred pH of most microbes? How does this knowledge relate to food preservation techniques?

-Neutral (5-8) -By increasing the acidic content (ie. Lactic acid buildup), reduces bacterial growth leaving the food with plenty of food value and little change to the quality or taste

How are microbes classified by pH?

-Neutralophiles -Acidophiles -Alkaliphiles

Heterotroph Catabolism

-Oxidation of C-H bonds releases energy (CH4 --> CO2) -NADH and FADH2 are electron carriers

What not to compost

-Pet waste -Fats/oils/grease/lard -Meat/bone -Pesticides -Dairy -Coal/Charcoal

Proton Motive Force purpose

-Powering complex molecular machines -Generates ATP by spinning the ATP synthase enzyme -Can also power flagellar rotation, uptake of nutrients, and efflux of toxic drugs

How are microbes classified by temperature?

-Psychrophiles -Mesophiles -Thermophiles -Hyperthermophiles

Normal growth conditions

-Sea level -Temperature 20-40C -Neutral pH -0.9% salt and ample nutrients

Photosystem II

-Separates an electron from bacteriochlorophyll itself -Electrons are then transferred to an ETC -Ultimately, an electron is returned to bacteriochlorophyll and *generates ATP* -*Has no direct way to make NADH or NADPH for biosynthesis* -Purple, non-sulfur bacteria

Photosystem I

-Separates electrons associated from H2S or succinate, Fe2+ -*Electrons are ultimately transferred to NAD+ or NADP+* (reduced carrier provides energy for CO2 fixation and biosynthesis) -Can also generate a net proton gradient to drive *ATP synthesis* -Green sulfur bacteria

What limits a cell's growth at low temperatures?

-Slow chemical reactions -Membrane inflexibility -Stuff freezes

Uses of Tephaflex

-Soft tissue reinforcement in plastic or reconstructive surgery -Temporary wound support -Reinforcement of soft tissue -Hernia repair

Isotonic solution

-Solutes are equal

Explain the importance of osmotic pressure to microbial growth. How does this knowledge relate to food preservation techniques?

-Water is critical to life, but environments differ in the amount of water available to growing organisms -More solutes in a solution means less water is available for microbes to use for growth -If solute concentration outside the cell is different from outside the cell, it can cause osmotic stress -By adding salt or sugar to food, it inhibits cell growth by reducing the amount of water available to the cell

Psychrophile temperature range

0-20C

Three functional components of the ETC

1. An initial substrate oxidoreductase 2. A mobile electron carrier 3. A terminal oxidase

Fruiting bodies

1. Binary fission (nutrient plentiful) 2. Gliding of cells when nutrients are depleted forming a mound of cells 3. Formation of fruiting body --> dispersal of dormant cells to new environment

Heterotrophy pathway from class

1. C-H bonds (glucose) ---> C=O bonds (CO2) -Glycolysis and TCA Cycle -Catabolism, oxidation 2. Reduced e- carriers (NADH, FADH2) ---> Oxidized e- carriers (NAD+, FAD) -ETC -Use e- carriers and produces PMF -O2 --> H2O (TEA) 3. PMF ---> ATP -ATP Synthase

Three major classes of prokaryotic energy-acquiring processes using an ETC

1. Chemotrophy -Organo -Litho 2. Phototrophy

Biofilm formation

1. Environmental signal causes bacteria to adhere to surface by means of flagella, pili, lipopolysaccharides, or other cell surface appendages 2. Coat the surface with polysaccharides in which other bacteria can attach 3. Lose their flagella and use twitching motility to move along surfaces; stop moving and attach to surface 4. More cells bind to surface and divide forming microcolonies 5. Communicate with each other through quorum sensing 6. Once concentration of signal is high enough, they begin to excrete exopolysaccharides 7. Mature biofilm 8. Dissolution and dispersion once nutrients are gone

Processes of Catabolism

1. Fermentation 2. Respiration 3. Photoheterotrophy

Glucose Breakdown Methods

1. Glycolysis (EMP) 2. Entner-Doudoroff Pathway 3. Pentose Phosphate Pathway 4. Fermentation

Outline the three different ways that ATP transfers energy.

1. Hydrolysis releasing phosphate (Pi) --The energy released by ATP hydrolysis can be transferred to a coupled reaction of biosynthesis, such as building an amino acid 2. Hydrolysis releasing pyrophosphate (PPi) --Yields twice as much energy 3. Phosphorylation of an organic molecule --No inorganic phosphate nor water molecule appears

How do cells minimize osmotic stress?

1. Move water through aquaporins 2. Protect their internal water in hypertonic media by synthesizing or importing compatible solutes (proline or K+) to prevent plasmolysis 3. In hypotonic media, pressure-sensitive (mechanosensitve) channels can be used to leak solutes out of the cell to prevent osmolysis

Autotrophy pathway from class

1. Oxidized e- carrier (NADP+) ---> Reduced e- carrier (NADPH) -ETC, Photosynthesis -Produces e- carriers and PMF 2. PMF ---> ATP -ATP synthase 3. C=O (CO2) ---> C-H (Glucose) -Reduction, anabolism -Calvin cycle

Proton circulation and pH homeostasis

1. Proton pumping through cytochromes establishes a PMF which drives flagellar rotation, ATP Synthase, and solute transport 2. Exchange extracellular K+ (in) for intracellular H+ (out) --pH too low 3. Can use Na+/H+ antiporters to bring in protons --pH too high --Na+ out and H+ in 4. Many microbes possess an emergency global response called acid tolerance or acid resistance

ETC Summary

1. The substrate oxidoreductase receives a pair of electrons from an organic substrate, such as NADH, or an inorganic substrate, such as H2 2. It donates the electrons to a mobile electron carrier, such as quinone -Quinone picks up 2H+ from the solution and is this reduced to quinol (QH2) 3. The oxidation of NADH and reduction of Q is coupled to pumping 4H+ across the membrane 4. A terminal oxidase complex receives the two electrons from QH2 -The 2H+ are transferred outside the membrane -The transfer of the two electrons through the terminal oxidase is coupled to pumping of 2H+ 5. The terminal oxidase complex transfer electrons to a terminal electron acceptor, such as O2

Half-life of caffeine

12 days

Mesophile temperature range

15-45C

Homolactic fermentation

2 molecules of lactic acid are produced

The typical temperature growth range usually spans the organism's optimal growth temperature by...

30-40 degrees

Carbon to Nitrogen ratio

30:1 Ratio of "browns" (C) to "greens" (N)

Thermophile temperature range

40-80C

Optimal pH

5.5-8.5

Windrow ideal height and width

6-10 feet high 12-20 feet wide Large enough to retain heat and moisture, but small enough for good air flow

Hyperthermophile temperature range

65-121C

When is decomposition most efficient? Too high or too low effects?

90-140F -High temperature are essential for breaking down proteins and lipids and killing off pathogens -Too low is when process considerably slows down -Too high: microorganisms cannot survive

Electron Transport System generates..

A proton motive force that drives protons across the membrane

Most energy-yielding reactions involved transfer of electrons from ________ to ________.

A reduced electron donor An oxidized electron acceptor

Lipids are broken down to...

Acetate

Caffeine binding

Adenosine binds to specific receptors and makes humans feel tired -Caffeine, which has a similar shape, binds to these receptors and blocks the binding of adenosine and stops the feeling of tiredness -Norepinephrine also binds to receptors and acts as a stimulant -With caffeine blocking the effects of adenosine, norepinephrine may be reduced and the brain relies on caffeine to remain alert

What happens to the carbons of glucose after TCA Cycle?

After the completion of the TCA Cycle, all carbons of glucose have been released as waste CO2

pH and enzyme activity

All enzyme activity exhibits optima, minima, and maxima with regards to pH

Peptides are hydrolyzed to...

Amino acids and then broken down to acetate, amines, and other molecules

How does temperature affect growth rates?

An increase of 10C can double growth rates.

pH and decomposition

As bacteria and fungi digest organic matter, they release organic acids -The resulting drop in pH encourages the growth of fungi and the breakdown of lignin and cellulose -Anaerobic conditions cause acid accumulation which limit bacterial activity

Biofilms

Assemblages of single-celled organisms attached to a surface and enclosed in a polysaccharide matrix secreted by the bacterial cells

Formation of an endospore

Asymmetrical cell division that produces a forespore and ultimately an endospore

Primary producers

Autotrophs -They convert CO2 into organism materials -Includes phototrophs (ie. sunlight run ETC) and chemotrophs (ie. chemicals run ETC) -Serve as food producers for consumers and decomposers

Where does the TCA Cycle take place?

Bacteria and archaea: Cytoplasm Eukaryotes: Mitochondria

Cell differentiation

Bacteria faced with environmental stress undergo complex molecular reprogramming that includes change in the cell structure -Endospore -Heterocysts -Fruiting bodies -Aerial hyphae

Why 30:1 ratio?

Bacteria have a C:N ration that is 6:1 and are 50% protein; the best ratio for compost is 30:1 because most of the carbon will be lost as CO2 in the process

How are microbes classified based on pressure?

Barophiles/piezophiles Barotolerant

Catabolism

Breakdown of complex molecules into smaller ones -Provides energy for anabolism - C-H --> C=O -Glycolysis and TCA Cycle

Thermophilic phase

Breakdown of proteins, fats, hemicellulose, and cellulose; mixed population of thermophiles

Autotrophy chemical equation

CO2 + H2O ---> O2 + C6H12O6 -CO2 is reduced (anabolism) -H2O is oxidized in the ETC

How are the Calvin Cycle and PPP related?

Calvin cycle is reductive PPP -PPP: Glucose + ADP + Pi + NADP+ = Ribose-5-P + CO2 + ATP + NADPH -Calvin cycle: Ribose-5-P + CO2 + ATP + NADPH = Glucose + ADP + Pi + NADP+

Strict aerobes

Can only grow in oxygen -Only uses oxygen as a TEA #1

Chemolithoautotroph

Carbon source: CO2 Energy source: Inorganic compounds, H2, Fe2+

Photoautotroph

Carbon source: CO2 Energy source: Light

Chemolithoheterotroph

Carbon source: Organic compounds Energy source: Inorganic compounds, H2, Fe2+

Chemoorganoheterotroph

Carbon source: Organic compounds (sugar, lipid, protein, etc.) Energy source: NADH, FADH2

NADH, FADH2

Carriers two or three times as much energy as ATP -Donates and accepts electrons -NADH, FADH2 are reduced forms -NAD+ and FAD are oxidized forms

ATP

Carries energy -Base, sugar, and three phosphates

Photoheterotrophy

Catabolism is conducted with a "boost" from light Photoheterotrophs, in this regard, are organisms that depend solely on light energy as they generate ATP through photophosphorylation. These organisms do not rely on carbon dioxide as their sole carbon source. They may use organic compounds such as carbohydrates, fatty acids, and alcohols they obtain from the environment for their carbon requirements.

Bacterial growth in nature

Cell sense changes and adjust to surroundings -Synthesize compounds useful for growth

Chemotrophy

Chemo = chemical to run ETC

Respiration

Complete breakdown of organic molecules with electron transfer to a terminal electron acceptor

Mineralization

Complete breakdown to phosphate, sulfur, ammonia, and CO2

How do microbes compensate for the low efficiency of fermentation?

Consume large quantities Fermentation yields little energy - need to go through fermentation many times to yield enough energy to produce biomass

Catalase

Converts H2O2 to H2O and O2

Superoxide dismutase

Converts superoxide (O2-) to H2O2 and O2

Reactive oxygen species

Damage cellular components (causing DNA mutations) -ROS examples: O2-, H2O2, HO-

Food chain

Decomposers create available nutrients in the soil for primary producers

Energy for photosynthesis

Derives from the photoexcitation of a light-absorbing pigment

Strict anaerobes

Die in the least bit of oxygen #2

Chemoorganoautotroph

Do not exist Carbon source: CO2 Energy source: NADH, FADH2

Windrow

Dome-shaped pile of organic matter

Endospores

Dormant, survival form of the organism resistant to high temperatures, disinfectants, desiccation (drying out), and starvation -Not everyone gets the chance -Cells evolved to DELAY sporulation AS LONG AS POSSIBLE (sporulation is LAST RESORT)

Natural convection

Driven by chimney effect -Warm air from center rises and is replaced by cool air from sides (brings in more O2)

Death phase

Dying -Total number of viable cells decrease -Cells die at constant rate -Exponential, but slower than cell growth -No division/synthesis -Does not produce anything new

Glycolysis is also known as the...

EMP Pathway -Embden/Meyerhof/Parnas Pathway

Sporulation

Endospore formation

Primary metabolites

Essential for growth, produced during exponential phase -Involved in metabolic processes such as respiration and photosynthesis

Autotrophs

Fix (reduces) CO2 and assemble into organic molecules (mainly sugars)

Detritus

Fresh or partially decomposed organic matter used as food Ex. Carcasses -Specialize in taking complex molecules like cellulose and breaking it down into molecules

Polysaccharides are hydrolyzed to...

Glucose -Poly --> di --> mono

Chemical equation for heterotrophic metabolism

Glucose + O2 --> CO2 + H2O -Glucose is oxidized (catabolism) -O2 is reduced

Aerotolerant anaerobes

Grow in oxygen while retaining a fermentation-based metabolism (anaerobic); NOT poisoned by oxygen #5

Microaerophiles

Grow only at lower O2 but still need O2 -Contain decreased levels of SOD and catalase #4

Log phase

Growing -Cells divide at a constant rate; growth is exponential -Generation time is measured -Production of primary metabolites such as EtOH, Lactic acid, pyruvate

Stationary phase

Growing=dying (both) -Nutrients are consumed, waste products accumulate -Total numbers remain constant -Become smaller, form endospores, new stress enzymes are produced to face the lack of food and changing environment -Secondary metabolites such as antibiotics (these molecules trigger endospore formation)

Biofilm structure

Have characteristic architectures -Channels through which nutrients and wastes pass -Cells communicate by synthesizing chemical signals

Decomposers

Heterotrophs -Digest the remains of the primary producers and consumers

Consumers

Heterotrophs -They use organic materials for metabolism and therefore rely on primary producers for food

Too high C:N ratio effects

High ratio (too little N): No significant population growth - temperature never rises

Oxygenic Z Pathway

Includes homologs of PS I and PS II -PSII ---> PSI -Photons are absorbed and electron pairs are removed from H2O and produce O2 -Oxygenic photosynthesis forms ATP, NADPH, O2 -Cyanobacteria and chloroplasts

ATP Synthase Input and Output, Location, and Purpose

Input: -ADP + Pi Output: -ATP Location: Thylakoid, cytoplasmic membrane Purpose: Create ATP using proton motive force

TCA Cycle Input and Output

Input: -Acetyl-CoA (2C) -NAD+ -FAD -ADP/GDP + Pi Output: -CO2 -NADH -FADH2 -ATP/GTP

Pentose Phosphate Pathway Input and Output

Input: -Glucose (6C) -NADP+ -ADP + Pi Output: -Ribose-5-phosphate (5C) -CO2 -NADPH -ATP

Pyruvate dehydrogenase complex (PDC) Input and Output

Input: -Pyruvate (3C) -NAD+ Output: -Acetyl-CoA (2C) -CO2 -NADH

Ethanol fermentation Input and Output

Input: -Pyruvate (3C) -NADH Output: -Ethanol (2C) -CO2 -NAD+

Lactic acid fermentation Input and Output

Input: -Pyruvate (3C) -NADH Output: -Lactic acid (3C) -NAD+

Calvin Cycle Input and Output

Input: -Ribose-5-Phosphate (5C) -CO2 -ATP -NADPH Output: -Glucose (6C) -ADP + Pi -NADP+

Anaerobic Lithotrophy ETC

Input: Electron donor: H2, Fe2+ TEA: CO2, SO42-, NO3- Output: -H+, Fe3+ -CH4, H2S, NO2-

Aerobic Lithotrophy ETC

Input: Electron donor: H2, Fe2+ TEA: O2 Output: -H+, Fe3+ -H2O

Aerobic Phototrophy ETC

Input: Electron donor: H2O TEA: NADP+ Output: -O2 -NADPH

Anaerobic Phototrophy ETC

Input: Electron donor: H2S TEA: NADP+ Output: -SO42- -NADPH

Anaerobic Organotrophy ETC

Input: Electron donor: NADH, FADH2 TEA: CO2, SO42-, NO3- Output: -NAD+, FAD -CH4, H2S, NO2-

Glycolysis Input and Output

Input: -Glucose (6C) -NAD+ -ADP + Pi Output: -Pyruvate (3C) x 2 -NADH -ATP

Aerobic Organotrophy ETC

Input: Electron donor: NADH, FADH2 TEA: O2 Output: -NAD+, FAD -H2O

Advantages of biofilms

Interaction can be cooperative: -Can foster growth of species that would not survive otherwise ---Strict anaerobes can grow in mouth if others consume O2 ---Metabolic waste of one can serve as nutrient for other Interactions can be competitive: -Some synthesize toxic compounds to inhibit competitors -Bioremediation -Enhances their resistance to antibiotics

Lithotrophy

Involved inorganic electron donors and inorganic or organic terminal electron acceptors Ex. H2, Fe2+

Phototroph

Involves light capture by chlorophyll, usually coupled to the splitting of H2S or H2O or organic molecules

Organotrophy

Involves organic electron donors and inorganic or organic terminal electron acceptors Ex. NADH, FADH2

How can oxygen be dangerous?

It is a very reactive species. -Can be poisonous to anaerobes

Extremophiles

Live in extreme environments (outside normal limits)

Calvin Cycle Location and Purpose

Location: Carboxysome Purpose: Anabolism of glucose by fixing CO2

Ethanol fermentation Location and Purpose

Location: Cytosol Purpose: Completes catabolism of sugar w/o using ETC or TEA Regenerates NAD+ for glycolysis

Lactic acid fermentation Location and Purpose

Location: Cytosol Purpose: Completes catabolism of sugar w/o using ETC or TEA Regenerates NAD+ for glycolysis

TCA Cycle Location and Purpose

Location: Cytosol Purpose: Completes glucose and other food metabolism

Pyruvate dehydrogenase complex (PDC) Location and Purpose

Location: Cytosol Purpose: Connects glycolysis and TCA cycle

Pentose Phosphate Pathway Location and Purpose

Location: Cytosol Purpose: Energy for lipid anabolism Sugar for nucleotide (RNA or DNA) anabolism

Glycolysis Location and Purpose

Location: Cytosol Purpose: Breaks sugar into 2 and sets-up other pathways

Second mesophilic stage

Long, slow degradation of lignin and other highly resistant compounds; mesophilic population

Too low C:N ratio effects

Low ratio (too much N): Ammonia and other odors

How does turning affect decomposition?

Makes everything better -Increases oxygen supply -Exposes new surfaces to decomposition -Keeps pile from becoming too hot -Gives thermophiles new food to eat

Binary fission

Most bacteria divide by binary fission, where one parent cell splits into two equal daughter cells

How do bacteria survive a range of pH?

Most maintain constant internal pH, typically near neutral -Pump out protons in acidic environment -Bring in protons in alkaline environment

Lag phase

Neither growing nor dying -Number of cells does not increase (NO DIVISION) -Sense environment and synthesize proper proteins for metabolism of resources that are available -Begin synthesizing macromolecules required for growth: DNAP, RNAP, ribosomes, DNA/RNA, enzymes, polysaccharides, lipids -Gear up to start using nutrients and dividing

Secondary metabolites

Not essential to survival, but may provide an advantage or enhancement -Produced when the cell is not operating under optimum conditions -Defense mechanisms: Antibiotics and endospore formation

Equation for cells undergoing binary fission..

Nt = No x 2^n Nt = final cell number No = original cell number n = number of generations

Biodiversity

Number and variety of species present and their evenness of distribution

What is in the compost?

Organic residues

Barophiles

Organisms adapted to grow at high pressures (up to 1000 atm/110 MPa)

How is oxygen beneficial?

Organisms can use oxygen as a TEA and extract energy from nutrients

Barotolerant

Organisms that grow well in 1-50 MPa

Location of ETC

Organotrophy/lithotrophy: -Cytoplasmic membrane Phototrophy: -Thylakoid membrane

Too large of windrow

Oxygen cannot penetrate the center

PDC and regulation

PDC activity is a key control point of metabolism -When carbon is plentiful, it is induced and Acetyl-CoA enters the TCA cycle

Which pathways in heterotrophic metabolism produce NADPH?

PPP

Fermentation

Partial breakdown of organic food without net electron transfer to an inorganic terminal electron acceptor

What adaptations must psychrophiles and thermophiles have that mesophiles do not have?

Phospholipid tails ---Psychro: Unsaturated (more double bonds) ---Thermo: Saturated (less double bonds) Proteins: ---Stronger interactions between protein folding ---More chaperone proteins DNA: ---More G/C bonds than A/T

Photoexcitation leads to...

Photolysis; the light-driven separation of an electron from a donor molecule such as H2O or H2S

Autotrophy pathways

Phototrophy: Light absorption --> Glucose (from CO2) Lithotrophy: Mineral oxidation --> Glucose (from CO2)

Ralstonia eutropha and Tephaflex

Polyhydroxyalkonates (polyester) are made naturally by soil bacteria called Ralstonia eutropha -They form storage granules of polyhyrdo... which can be made into sutures and they can be absorbed by the body GROW VERY SLOWLY

Heterotrophy pathway

Polysaccharides --> Glucose (6C) --> Pyruvate (3C) --> Acetyl-CoA (2C) --> TCA Cycle Lipids and peptides --> Acetate (2C) --> CO2 + H2O

Facultative anaerobes

Possess both the ability for fermentative metabolism and respiration (anaerobic and aerobic); aerobic is better so they congregate on top #3

Surface ponding

Problem: Depressions or ruts Inadequate slope Solution: Fill depression and/or re-grade Grade site to recommended slope design

Anaerobic odor Problem and solution

Problem: Excess moisture Window too large Temperature > than 140° F Leaf compaction Solutions: Turn windrow Make windrow smaller Eliminate ponding

Fires/spontaneous combustion

Problem: Excessive temperature Inadequate moisture Stray sparks, cigarettes, etc. Solution: Make windrow smaller Add water Keep potential fire sources away from windrows

Runoff - pollution of surface waters

Problem: Leachate discharge Solution: Avoid surface runoff / Treat leachate before it leaves site by passing through soil, sand, or grass

Vectors: rats and mosquitos

Problem: Presence of garbage (food, etc.) Presence of stagnant water Not enough aeration Solution: Fill depression and/or re-grade Grade site to recommended slope design Turn windrow

High temperature Problem and Solution

Problem: Windrow too large Leaf compaction Solution: Reduce windrow size Turn windrow

Low temperature Problem and Solution

Problem: Windrow too small Insufficient moisture Poor aeration Solution: Combine windrows Add water Turn Windrow

Heterolactic fermentation

Produces 1 lactic acid, 1 EtOH, 1 CO2

Mixed-acid fermentation

Produces acetate, formate, lactate, and succinate, EtOH, H2, CO2

Caffeine role in plants

Protection -Kills snails and other organisms that cannot handle caffeine content

First mesophilic phase

Rapid uptake of soluble sugars and starches; explosive growth of mesophilic bacteria

Anabolism

Reactions that build cells -C=O --> C-H -Calvin Cycle

Electrons move from...

Reduced food molecules onto energy carriers, then onto membrane protein carriers, and then onto oxygen or oxidized materials Food --> e- carriers --> Proteins in ETC --> TEA

Fermentation and energy

Releases energy from the oxidation of NADH to NAD+

Halophiles

Require high salt concentrations (10-20% NaCl)

Germination

Return to vegetative state (will not until in favorable environment)

Oxygen and windrow

Shape of the windrow supports oxygen flow and aerobic respiration *Anaerobic metabolism is slow and produces methane, hydrogen sulfide, and acids which attract rodents and disease vectors

Heterocysts

Specialized cells used for nitrogen fixation to ammonia -Produced when organism is nitrogen deprived -Differentiate from individual cells in filament -Thick heterocyst wall prevents O2 diffusion into heterocyst which would inactivate nitrogenase

Aerial hyphae

Spore -germination--> germinating spore -vegetative growth--> vegetative mycelium -aerial growth--> aerial hyphae -sporulation--> spore chains -Produce antibiotics and feast on dead cells -Form spores resistant to drying out as nutrients deplete and disperse

Which bacteria lack the SOD and catalase enzyme?

Strict anaerobes

Tephaflex

Surgical sutures made by bacteria -Can be made into sutures, fils, and textile products