Exam 2 Web-Only Edit Flashcards
Metabolism [Definition] (10.1)
- All chemical reactions in a cell.
- catbolism + anabolism = metabolism
- Requires the flow of energy (capacity to do work) and the participation of enzymes
Catabolism [Definition] (10.1)
Breakdown of complex molecules into smaller ones with release of energy for anabolism
Anabolism [Definition] (10.1)
Reactions that build cells
What does ATP stand for? (10.2)
Adenosine Triphosphate
What does the amount of Gibbs Free Energy (∆G) determine in a reaction? (10.2)
∆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.
What is Gibbs Free Energy determined by? (10.2)
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).
What does Gibbs free energy measure? (10.2)
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)
Why does a chemical reaction occur spontaneously?
A process tends to occur spontaneously only if ∆G is negative.
What do solutes (such as sugar / salt) do to the availability of water? (7.3)
- 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 (aw):
Higher solute = Lower aw
Hypotonic (7.3)
- Low extracellular solute concentration
- Water flowing into the cell
- Ex: Freshwater lakes & streams
Isotonic (7.3)
-Same concentration of solute both in & out of the cell
Hypertonic (7.3)
- High extracellular solute concentration-Water flowing out of the cell
- Low aw
- 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
Describe water activity
The water activity (aw) 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 (Psoln) to that of pure water (Pwater)· Distilled water has an aw of 1, milk has an aw of 0.97, a saturated salt solution has an aw of 0.75, and the aw of dried fruits is only about 0.5.
Halobacterium [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
Staphylococcus [bacteria] (7.3)
- A halotolerant
- Found on human skin
- Isolated using Mannitol Salt Agar
aw
The water activity (aw) 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 (Psolution) to that of pure water (Pwater)· Distilled water has an aw of 1, milk has an aw of 0.97, a saturated salt solution has an aw of 0.75, and the aw of dried fruits is only about 0.5.
Compatible Solutes (7.3)
- 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.
What are the two types of extremophiles that can withstand strong pHs? (7.3)
- 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
General features of a biofilm (7.4)
- Microbial community
- Attached to a surface
- Covered with a matrix of polysaccharide, DNA, & protein—“Protective Matrix”
- The cells + The Protective Matrix = Biofilm
- Negatively charged
Four Stages of Biofilm Formation (7.4)
1) Attachment
2) Colonization
3) Maturation
4) Dispersal
Attachment - Biofilm Formation Stage (7.4)
- 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.
Colonization - Biofilm Formation Stage (7.4)
- 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
Maturation - Biofilm Formation Stage (7.4)
-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.
Dispersal - Biofilm Formation Stage (7.4)
- Fourth / Final stage-Reactivation of motility
- Allows the bacteria to spread out again
Dental plaque (7.4)
- A biofilm
- Bacterial film on tooth surface (over 300 microbial species)
Caries (7.4)
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
Periodontal disease (7.4)
-A biofilm-Inflammation & tissue destruction
What are two microbes responsible for caries discussed in class (7.4)?
- Streptococcus mutans*
- Poryphromonas gingivalis*
- Both cause damage due to fermentation
How is ATP created in aerobic & anaerobic respiration? (10.3)
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.
How is ATP created in fermentation? How does this differ from respiration? (10.3)
In fermentation (and glycolysis, TCA “Krebs” cycle), ATP is created via substrate-level phosphorylation. During respiration, ATP is generated via oxidative phosphorylation.
How is ATP created in photosynthesis? (10.3)
ATP is created via photophosphorylation
Exergonic reaction (10.2)
-Favors products
∆G°’ is negative, release of energy
Endergonic reaction (10.2)
-Favors reactants
∆G°’ is positive, requires energy input
Oxidation - Reduction Rxns [general] (10.3)
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.
O.I.L.R.I.G.
LEO the lion says GER
(10.3)
OxidationIsLossReductionIsGain
Loosing Electrons is Oxidation, Gaining Electrons is Reduction
–Oxidation: Removal of e-
—Substance that is oxidized in the donor
–Reduction: Addition of e-
—Substance that is reduced is the acceptor
In the following reaction, what is oxidized? Reduced? What enzyme is required to catalyze the reaction? (10.3)[Malate + NAD+] —–> [Oxaloacetate + NADH + H+]
Oxidized: Malate—Oxidized to oxaloacetateReduced: NAD+—Reduced to NADHEnzyme: Malate Dehydrogenase
Rhodoferax metabolins [bacteria] (10.3)
-Psychrophilic, obligate anaerobe that oxidizes acetate w/ the reduction of iron—Habitat: Cold, no oxygen—Donor:Acetate—Acceptor: Iron
Enzymes (10.6)
-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
How do Enzymes Lower Activation Energy? (10.6)
-Increase local concentrations of substrates-Orient substrates properly for reactions to proceed
Reduction Potential [E(0)] (10.3)
-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
What does a redox reaction accomplish? (10.3)
It pairs molecules with a negative E(0) to molecules with a positive E(0)
Electron Tower (10.3)
-Reference fig. 10.6-Negative delta G’ - Better e- donors-Positive delta G’ - Better e- acceptors
How do microbes transfer energy [4 steps]? (10.4)
-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
What are the two types of electron carriers? (10.4)
-Freely diffusable—Ex: NAD+ & NADP+-Membrane-bound—Ex: Flavoproteins, cytochromes, quinones
What does NAD+ stand for? (10.4)
Nicotinamide Adenine Dinucleotide
What does NADP stand for? (10.4)
Nicotinamide Adenine Dinucleotide Phosphate
What do the reduced forms of NAD+ & NADP look like? What do they do for the cell? (10.4)
-Reduced forms:—NAD: NADH—NADP: NADPH-These reduced forms are the “reducing power” of the cell
Quinones (10.4)
-A membrane-bound carrier-Made of organic compounds-Ex: Coenzyme Q
Cytochromes (10.4)
-A membrane-bound carrier-Made of proteins-Use iron to transfer electrons—Iron is part of a heme group
What are the two types of metabolic groups in the carbon cycle? (11.1)
-Heterotrophs-Autotrophs
Heterotrophs (11.1)
-Use reduced, preformed organic compounds as their source of carbon-Convert huge amounts of C –> CO2-Ex: Animals, many kinds of microbes
Autotrophs (11.1)
-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
Phototrophs (11.1)
-Use light as a source of energy
Chemotrophs (11.1)
-Oxidize chemical compounds as source of energy-Often the same chemicals that are used for the carbon source
Lithotrophs (11.1)
-Use inorganic molecules as their source of electron donors-Use respiration to accept electrons-Table 11.1 & 11.2
Organotrophs (11.1)
-Use organic molecules as their source of electron donors-Use fermentation to accept electrons-Table 11.1 & 11.2
What would a photolithoautotroph use for a source of energy? Electrons? Carbon? (11.1)
-Energy : Light (photo)-Electrons: Inorganic compounds (litho)-Carbon: CO2 (auto)
What kinds of organisms are lithotrophs? (11.1)
-Microbes (prokaryotes) exclusively—Eukaryotes are either photoautotrophs or heterotrophs
What are the three basic needs that fulfill all sources of energy, carbon, and electrons? (11.1)
1) ATP as energy currency2) Reducing power to supply electrons for chemical reactions3) Precursor metabolites for biosynthesis
What is the name for a microbe prefers to grow in solutions with partial pressures lower than that of pure water?
The ratio of the partial pressure of the solution (Psolution) to the partial pressure of pure water (Pwater) is known as the water activity (aw). Values of aw lower than one indicate a hypertonic environment. While osmotolerant organisms are capable of growing in this environment, osmophilic organisms prefer this environment, some tolerating aw of only 0.6.
What is the difference between a halotolerant microbe and a halophilic microbe?
In contrast to osmotolerant microbes (which grow best at aw closer to 1 but can stand less), osmophilic microbes (e.g., halophilic Halobacterium spp.) grow best at low aw.
What is the genus of the halophilic archaea from class notes?
- 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
What is the genus of the halotolerant bacteria from class notes?
- Staphylococcus*
- A bacteria (7.3)
- A halotolerant
- Found on human skin
- Isolated using Mannitol Salt Agar
EPS (7.4)
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.
Describe the difference between ∆G, ∆G° and ∆G°’
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 Keq is given by this equation.
