Exam 2 Web-Only Edit

Question 1

Metabolism [Definition] (10.1)

Answer 1

• All chemical reactions in a cell.
• catbolism + anabolism = metabolism
• Requires the flow of energy (capacity to do work) and the participation of enzymes

Question 2

Catabolism [Definition] (10.1)

Answer 2

Breakdown of complex molecules into smaller ones with release of energy for anabolism

Question 3

Anabolism [Definition] (10.1)

Answer 3

Reactions that build cells

Question 4

What does ATP stand for? (10.2)

Answer 4

Adenosine Triphosphate

Question 5

What does the amount of Gibbs Free Energy (∆G) determine in a reaction? (10.2)

Answer 5

∆G (Gibbs free energy change) expresses the amount of energy capable of doing work during a reaction at constant temperature and pressure.

When a reaction proceeds with the release of free energy, ∆G is negative and the reaction is said to be exergonic.

In endergonic reactions, the system gains free energy and ∆G is positive.

Question 6

What is Gibbs Free Energy determined by? (10.2)

Answer 6

When a chemical reaction occurs at constant temperature, the free-energy change, ∆G, is determined by two things:

• the enthalpy change, ∆H, negative for a reaction that releases heat (∆H reflects bond formation and noncovalent interactions).
• the entropy change, ∆S, positive for a reaction that increases the system’s randomness (a function of temperature).

Question 7

What does Gibbs free energy measure? (10.2)

Answer 7

The potential for a reaction to spontaneously proceed. Reactions that are favourable (negative ∆Gs, exergonic, catabolism) can be coupled to reactions that would not normally proceed (positive ∆Gs, endergonic, anabolism)

Question 8

Why does a chemical reaction occur spontaneously?

Answer 8

A process tends to occur spontaneously only if ∆G is negative.

Question 9

What do solutes (such as sugar / salt) do to the availability of water? (7.3)

Answer 9

• Solutes decrease the availability of water to microbes because the water is “tied up” by its interaction with the solutes.
• Availability of water affects growth of all cells
• Expressed as water activity (a_w):

Higher solute = Lower a_w

Question 10

Hypotonic (7.3)

Answer 10

• Low extracellular solute concentration
• Water flowing into the cell
• Ex: Freshwater lakes & streams

Question 11

Isotonic (7.3)

Answer 11

-Same concentration of solute both in & out of the cell

Question 12

Hypertonic (7.3)

Answer 12

• High extracellular solute concentration-Water flowing out of the cell
• Low a_w
• Ex: Dead Sea, Great Salt Lake, Peanut butte
• Osmophiles live in these conditions
• Microbes living in these conditions have compatible solutes in an effort to increase the materials inside the cell

Question 13

Describe water activity

Answer 13

The water activity (a_w) of a solution is 1/100 the relative humidity of the solution (when expressed as a percent). It is also equivalent to the ratio of the solution’s vapor pressure (P_soln) to that of pure water (P_water)· Distilled water has an a_w of 1, milk has an a_w of 0.97, a saturated salt solution has an a_w of 0.75, and the a_w of dried fruits is only about 0.5.

Question 14

Halobacterium [archaea] (7.3)

Answer 14

• A halophile
• Cause of pink coloration to Pink Lake in Australia—Yes, this is an archaea even though it has ‘bacterium’ in its name

Question 15

Staphylococcus [bacteria] (7.3)

Answer 15

• A halotolerant
• Found on human skin
• Isolated using Mannitol Salt Agar

Question 16

a_w

Answer 16

The water activity (a_w) of a solution is 1/100 the relative humidity of the solution (when expressed as a percent). It is also equivalent to the ratio of the solution’s vapor pressure (P_solution) to that of pure water (P_water)· Distilled water has an a_w of 1, milk has an a_w of 0.97, a saturated salt solution has an a_w of 0.75, and the a_w of dried fruits is only about 0.5.

Question 17

Compatible Solutes (7.3)

Answer 17

• Compatible solutes (also called osmoprotectants) are molecules that can be kept at high intracellular concentrations without in­ terfering with metabolism and growth.
• Help halophiles (and other osmophiles) to survive under high salt (or other solute) concentrations.

Further reading:

Osmoprotectants or compatible solutes are small molecules that act as osmolytes and help organisms survive extreme osmotic stress. In plants, their accumulation can increase survival under stress e.g. drought. Examples of compatible solutes include betaines, amino acids, and the sugar trehalose. These molecules accumulate in cells and balance the osmotic difference between the cell’s surroundings and the cytosol. In extreme cases, such as in bdelloid rotifers, tardigrades, brine shrimp, and nematodes, these molecules can allow cells to survive being completely dried out and let them enter a state of suspended animation called cryptobiosis. In this state the cytosol and osmoprotectants become a glass-like solid that helps stabilize proteins and cell membranes from the damaging effects of desiccation.

Question 18

What are the two types of extremophiles that can withstand strong pHs? (7.3)

Answer 18

• Alkaliphiles—Withstand high pH (basic conditions)
• Acidophiles—Withstand low pH (acidic conditions)

—Ex: E. coli can withstand pH of 2 - 10 — very wide range, though not typically thought of as an extremophile

Question 19

General features of a biofilm (7.4)

Answer 19

• Microbial community
• Attached to a surface
• Covered with a matrix of polysaccharide, DNA, & protein—“Protective Matrix”
• The cells + The Protective Matrix = Biofilm
• Negatively charged

Question 20

Four Stages of Biofilm Formation (7.4)

Answer 20

1) Attachment
2) Colonization
3) Maturation
4) Dispersal

Question 21

Attachment - Biofilm Formation Stage (7.4)

Answer 21

• First stage
• Use of pili & adherence proteins

Initially microbes attach to the conditioned surface but can readily detach. Eventually they form a slimy ma­trix made up of various polymers, depending on the microbes in the biofilm. The polymers are collectively called extracellular polymeric substances (EPS), and they include polysaccharides, proteins, glycoproteins, glycolipids, and DNA. The EPS matrix allows the microbes to stick more stably to the surface.

Question 22

Colonization - Biofilm Formation Stage (7.4)

Answer 22

• Second stage
• Quorum sensing—Cell-cell signaling that is density dependent
• Activates gene expression—Genes that make the Protective Matrix (EPS, extracellular polymeric substances) are turned on

Question 23

Maturation - Biofilm Formation Stage (7.4)

Answer 23

-Third stage-Forms a “mushroom” with:

—Channels for nutrients

—Oxygen gradients

A mature biofilm is a complex, dynamic community of micro­organisms. It exhibits considerable heterogeneity due to differences in the metabolic activity of microbes at various locations within the biofilm; some are persister cells (Fig 7.17, below). Biofilm microbes in­ teract in a variety of ways. For instance, the waste products of one microbe may be the energy source for another microbe. e cells also use molecules to communicate with each other, as we describe next. Finally, DNA present in the EPS can be taken up by members of the bio lm community. us genes can be transferred from one cell (or species) to another.

Question 24

Dispersal - Biofilm Formation Stage (7.4)

Answer 24

• Fourth / Final stage-Reactivation of motility
• Allows the bacteria to spread out again

Question 25

Dental plaque (7.4)

Answer 25

- A biofilm - Bacterial film on tooth surface (over 300 microbial species)

Question 26

Caries (7.4)

Answer 26

Dental caries, also known as tooth decay, **cavities**, or caries, is a breakdown of teeth due to activities of bacteria. - Caused by a biofilm - Tooth decay - Bacterial fermentation --\> Acidic products --\> Damage to enamel ---*Streptococcus mutans* - fermentation ---*Poryphromonas gingivalis* - fermentation

Question 27

Periodontal disease (7.4)

Answer 27

-A biofilm-Inflammation & tissue destruction

Question 28

What are two microbes responsible for caries discussed in class (7.4)?

Answer 28

* Streptococcus mutans* * Poryphromonas gingivalis* - Both cause damage due to fermentation

Question 29

How is ATP created in aerobic & anaerobic respiration? (10.3)

Answer 29

In all cases of respiration, ATP is created via oxidative phosphorylation. The final electron acceptor may differ, in aerobic respiration the final acceptor is O₂.

Question 30

How is ATP created in fermentation? How does this differ from respiration? (10.3)

Answer 30

In fermentation (and glycolysis, TCA "Krebs" cycle), ATP is created via substrate-level phosphorylation. During respiration, ATP is generated via oxidative phosphorylation.

Question 31

How is ATP created in photosynthesis? (10.3)

Answer 31

ATP is created via photophosphorylation

Question 32

Exergonic reaction (10.2)

Answer 32

-Favors products ∆G°' is negative, release of energy

Question 33

Endergonic reaction (10.2)

Answer 33

-Favors reactants ∆G°' is positive, requires energy input

Question 34

Oxidation - Reduction Rxns [general] (10.3)

Answer 34

A reduction reaction always occurs with an oxidation reaction. Redox reactions include all chemical reactions in which atoms have their oxidation state changed; in general, redox reactions involve the transfer of electrons between chemical species. The chemical species from which the electron is stripped (the donor) is said to have been oxidized, while the chemical species to which the electron is added (the acceptor) is said to have been reduced. Oxygen is not necessarily included in such reactions as other chemical species can serve the same function.

Question 35

O.I.L.R.I.G. LEO the lion says GER (10.3)

Answer 35

**O**xidation**I**s**L**oss**R**eduction**I**s**G**ain **L**oosing **E**lectrons is **O**xidation, **G**aining **E**lectrons is **R**eduction --Oxidation: Removal of e^- ---Substance that is oxidized in the donor --Reduction: Addition of e^- ---Substance that is reduced is the acceptor

Question 36

In the following reaction, what is oxidized? Reduced? What enzyme is required to catalyze the reaction? (10.3)[Malate + NAD+] -----\> [Oxaloacetate + NADH + H+]

Answer 36

Oxidized: Malate---Oxidized to oxaloacetateReduced: NAD+---Reduced to NADHEnzyme: Malate Dehydrogenase

Question 37

Rhodoferax metabolins [bacteria] (10.3)

Answer 37

-Psychrophilic, obligate anaerobe that oxidizes acetate w/ the reduction of iron---Habitat: Cold, no oxygen---Donor:Acetate---Acceptor: Iron

Question 38

Enzymes (10.6)

Answer 38

-Proteins (usually) that catalyze reactions---Ribozymes: catalytic RNAs-Act on substrates & convert to products-Require activation energy to bring reacting molecules together-Increase the rate of reaction by lowering the activation energy-Often named for the reactions that they catalyze---Ex: Phophotase, Kinase, Cellulase

Question 39

How do Enzymes Lower Activation Energy? (10.6)

Answer 39

-Increase local concentrations of substrates-Orient substrates properly for reactions to proceed

Question 40

Reduction Potential [E(0)] (10.3)

Answer 40

-Equillibirum constant for redox rxns-Measure the tendency of the donor to lose electrons-More negative E(0) is a better donor-More positive E(0) is a better acceptor

Question 41

What does a redox reaction accomplish? (10.3)

Answer 41

It pairs molecules with a negative E(0) to molecules with a positive E(0)

Question 42

Electron Tower (10.3)

Answer 42

-Reference fig. 10.6-Negative delta G' - Better e- donors-Positive delta G' - Better e- acceptors

Question 43

How do microbes transfer energy [4 steps]? (10.4)

Answer 43

-Microbes transfer energy by moving electrons from:---Reduced food molecules (glucose) --\>---Diffusable carriers in the cytoplasm --\>---Membrane-bound carriers --\>---O2, Metals, or oxidized forms of N & SOverall: From food to O2, Metals, or oxidized N & S

Question 44

What are the two types of electron carriers? (10.4)

Answer 44

-Freely diffusable---Ex: NAD+ & NADP+-Membrane-bound---Ex: Flavoproteins, cytochromes, quinones

Question 45

What does NAD⁺ stand for? (10.4)

Answer 45

Nicotinamide Adenine Dinucleotide

Question 46

What does NADP stand for? (10.4)

Answer 46

Nicotinamide Adenine Dinucleotide Phosphate

Question 47

What do the reduced forms of NAD⁺ & NADP look like? What do they do for the cell? (10.4)

Answer 47

-Reduced forms:---NAD: NADH---NADP: NADPH-These reduced forms are the "reducing power" of the cell

Question 48

Quinones (10.4)

Answer 48

-A membrane-bound carrier-Made of organic compounds-Ex: Coenzyme Q

Question 49

Cytochromes (10.4)

Answer 49

-A membrane-bound carrier-Made of proteins-Use iron to transfer electrons---Iron is part of a heme group

Question 50

What are the two types of metabolic groups in the carbon cycle? (11.1)

Answer 50

-Heterotrophs-Autotrophs

Question 51

Heterotrophs (11.1)

Answer 51

-Use reduced, preformed organic compounds as their source of carbon-Convert huge amounts of C --\> CO2-Ex: Animals, many kinds of microbes

Question 52

Autotrophs (11.1)

Answer 52

-Use CO2 as their source of carbon-Synthesize organic compounds that are used by heterotrophs-Also called Primary Producers-Ex: Plants, many kinds of microbes

Question 53

Phototrophs (11.1)

Answer 53

-Use light as a source of energy

Question 54

Chemotrophs (11.1)

Answer 54

-Oxidize chemical compounds as source of energy-Often the same chemicals that are used for the carbon source

Question 55

Lithotrophs (11.1)

Answer 55

-Use inorganic molecules as their source of electron donors-Use respiration to accept electrons-Table 11.1 & 11.2

Question 56

Organotrophs (11.1)

Answer 56

-Use organic molecules as their source of electron donors-Use fermentation to accept electrons-Table 11.1 & 11.2

Question 57

What would a photolithoautotroph use for a source of energy? Electrons? Carbon? (11.1)

Answer 57

-Energy : Light (photo)-Electrons: Inorganic compounds (litho)-Carbon: CO2 (auto)

Question 58

What kinds of organisms are lithotrophs? (11.1)

Answer 58

-Microbes (prokaryotes) exclusively---Eukaryotes are either photoautotrophs or heterotrophs

Question 59

What are the three basic needs that fulfill all sources of energy, carbon, and electrons? (11.1)

Answer 59

1) ATP as energy currency2) Reducing power to supply electrons for chemical reactions3) Precursor metabolites for biosynthesis

Question 60

What is the name for a microbe prefers to grow in solutions with partial pressures lower than that of pure water?

Answer 60

The ratio of the partial pressure of the solution (P_solution) to the partial pressure of pure water (P_water) is known as the water activity (a_w). Values of a_w lower than one indicate a hypertonic environment. While osmotolerant organisms are capable of growing in this environment, osmophilic organisms prefer this environment, some tolerating a_w of only 0.6.

Question 61

What is the difference between a halotolerant microbe and a halophilic microbe?

Answer 61

In contrast to osmotolerant microbes (which grow best at a_w closer to 1 but can stand less), osmo­philic microbes (e.g., halophilic *Halobacterium* spp.) grow best at low a_w.

Question 62

What is the genus of the halophilic archaea from class notes?

Answer 62

* Halobacterium* - An archaea (7.3) - A halophile - Cause of pink coloration to Pink Lake in Australia---Yes, this is an archaea even though it has 'bacterium' in its name

Question 63

What is the genus of the halotolerant bacteria from class notes?

Answer 63

* Staphylococcus* - A bacteria (7.3) - A halotolerant - Found on human skin - Isolated using Mannitol Salt Agar

Question 65

EPS (7.4)

Answer 65

The polymers that make up the protective matrix are collectively called **extracellular polymeric substances** (EPS), and they include _polysaccharides, proteins, glycoproteins, glycolipids, and DNA_. The EPS matrix allows the microbes to stick more stably to the surface. As the biofilm thickens and matures, the microbes reproduce and secrete additional polymers.

Question 66

Describe the difference between ∆G, ∆G° and ∆G°'

Answer 66

When the free energy change for a process is determined at carefully defined standard conditions of concen­tration, pressure, pH, and temperature, it is called the standard free energy change (∆G°). If the pH is set at 7.0 (which is close to the pH of living cells), the standard free energy change is indicated by the symbol G°'. The change in standard free energy may be thought of as the maximum amount of energy available from the system for useful work under standard conditions. Using ∆G°' values allows comparisons of reactions without considering varia­tions in G due to di erences in environmental conditions. e relationship between G' and K_eq is given by this equation.