microbiology ch.6

Dehydrogenation

= oxidation

Hydrogenation

= reduction

In the process of oxidative phosphorylation, the energy of proton motive force is used to generate a) NADH. b) ADP. c) ethanol. d) ATP. e)glucose.

ATP

Which of these is not a coenzyme? a) FAD b) Coenzyme A c) NAD+ d) ATP e) NADP+

ATP

harvesting energy

Photosynthetic organisms harvest energy in sunlight Power synthesis of organic compounds from CO2 Convert kinetic energy of photons to potential energy of chemical bonds

What would happen if ribulose 1,5-bisphosphate (RuBP) were depleted in a cell?

The Calvin cycle would stop.

Fermentation is used as a means of preserving foods. Why would it slow spoilage?

The acids produced inhibit many spoilage organisms.

How would cellulose-degrading bacteria in the rumen of a cow benefit the animal?

They break down cellulose, allowing cows to use the component subunits. Cows do not produce cellulase. Without the bacteria, cows could not digest cellulose.

Explain why sulfa drugs prevent bacterial growth without harming the human host.

They competitively inhibit an enzyme that is unique to microorganisms; human cells lack the enzyme, and therefore are not harmed.

Which of the following statements is false? Enzymes... a) bind to substrates. b) lower the energy of activation. c) convert coenzymes to products. d) speed up biochemical reactions. e) can be named after the kinds of reaction they catalyze.

convert coenzymes to products.

kinetic energy

energy of movement (e.g., moving water)

photosynthesis

plants, algae, several groups of bacteria 6 CO2 + 12 H2X ------->C6H12O6 + 12 X + 6 H2O where X indicates element such as oxygen or sulfur

Endergonic reactions

products have more free energy Reaction requires input of energy

Exergonic reactions:

reactants have more free energy Energy is released in reaction

potential energy

stored energy (e.g., chemical bonds, rock on hill, water behind dam)

energy

the capacity to do work

Degradation of fats as an energy source involves all of the following except a) β-oxidation. b) acetyl-CoA. c) glycerol. d) lipase. e) transamination.

transamination.

Respiration

transfers electrons from glucose to electron transport chain

Organic, inorganic compounds

used as energy source

O2, other molecules

used as terminal electron acceptor

A worker in a cheese-making facility argues that whey, a nutrient-rich by-product of cheese, should be dumped in a nearby pond where it could serve as fish food. Explain why this proposed action could actually kill the fish by depleting the O2 in the pond.

Aerobic microorganisms would use the whey as an energy source, breaking it down to CO2 and using O2 as a terminal electrons acceptor. This would deplete the dissolved O2 in the water; without adequate O2, the fish would die.

Why do cells secrete hydrolytic enzymes?

Because they cannot bring most macromolecules into the cell. By secreting hydrolytic enzymes they break the macromolecules into their component subunits, which can be transported into the cell.

Anabolism

Biosynthetic processes Assemble subunits of macromolecules Use ATP to drive reactions

In the TCA cycle, the carbon atoms contained in acetate are con¬verted into a) lactic acid. b) glucose. c) glycerol. d) CO2.n e) all of these.

CO2.n

In photosynthesis, what is encompassed by the term "light-independent reactions"?

Carbon fixation

Explain the difference between catabolism and anabolism.

Catabolism breaks down compounds to release their energy; anabolism uses energy to make compounds.

Explain the function of a coenzyme.

Coenzymes carry molecules or electrons.

cytochromes

Contain heme, molecule with iron atom at center Several types

glycolysis steps

Converts 1 glucose to 2 pyruvates; yields net 2 ATP, 2 NADH Investment phase: 2 phosphate groups added Glucose split to two 3-carbon molecules Pay-off phase: 3-carbon molecules converted to pyruvate Generates 4 ATP, 2 NADH total

Scientists working with DNA in vitro often store it in solutions that contain EDTA, a chelating agent that binds magnesium (Mg2+). This is done to prevent enzymes called DNases from degrading the DNA. Explain why EDTA would interfere with enzyme activity.

DNases require magnesium as a cofactor. By binding magnesium, EDTA scavenges the available cofactor, preventing enzyme activity

tricarboxylic acid cycle or TAC

Oxidizes pyruvates from glycolysis Generates reducing power, precursor metabolites, ATP

Why is the overall ATP yield in aerobic respiration only a theoretical number?

Different prokaryotes have different components to their electron transport chain, and proton motive force can be used for purposes other than ATP generation. Electrons cannot exist free in solution, so oxidations and reductions are linked; an enzyme that oxidizes one substance reduces another.

How does the fate of electrons carried by NADPH differ from the fate of electrons carried by NADH?

Electrons carried by NADPH are used in biosynthesis whereas those carried by NADH are passed to the electron transport chain.

Allosteric Regulation

Enzyme activity controlled by binding to allosteric site Distorts enzyme shape, prevents or enhances binding Regulatory molecule is usually end product Allows feedback inhibition

(ATP) Substrate-level phosphorylation

Exergonic reaction powers

Why do the electrons carried by FADH2 result in less ATP produc¬tion than those carried by NADH?

FADH2 has a higher affinity for electrons that NADH does, so the electrons it carries must be transferred to an even higher affinity molecule; it's electrons are transferred to Complex II of the electron transport chain, which is "downstream" or "downstairs" of Complex I (the complex to which NADH transfers its electrons).

Which compound contains more free energy—glucose or oxaloacetate? On what did you base your conclusion?

Glucose. It has less affinity for its electrons (see figure 6.7).It is part of the electron transport chain.

glucose to O2

Greater affinity for electrons Energy released when electrons move from low affinity molecule to high affinity molecule

Which energy source, Fe2+ or H2S, would result in the greatest energy yield when O2 is used as a terminal electron acceptor (hint: refer to figure 6.7)?

H2S

Fermentation

If cells cannot respire, will run out of carriers available to accept electrons Glycolysis will stopFermentation uses pyruvate or derivative as terminal electron acceptor to regenerate NAD+

How does the "investment phase" of glycolysis effect the net yield of ATP in that pathway?

If energy were not spent in the "investment phase" then all four ATPs made in the "payoff phase" could be used for other purposes.

With a branched biochemical pathway, why would it be important for a cell to shut down the first step as well as branching steps?

If the cell couldn't do that, and it had sufficient levels of the endproducts of the pathway, then the product of the step before the branch would accumulate.

Why does fermentation supply less energy than respiration?

It does not oxidize glucose completely; the electrons are passed to an intermediate in the breakdown process.

How does ATP serve as a carrier of free energy?

It has unstable phosphate bonds that are easily broken; cells have enzymes that help break those bonds to release the energy

β-carotene is a carotenoid that mammals can use as a source of vitamin A. What is the function of carotenoids in photosynthetic organisms?

It is an accessory pigment that captures the radiant energy.

What is the role of rubisco?

It is the enzyme in the Calvin cycle that joins CO2 to an organic compound.

Explain why glutamate synthesis is particularly important for a cell.

It provides a way for cells to incorporate ammonium into organic material.

quinones

Lipid-soluble molecules Move freely, can transfer electrons between complexes

Name three food products produced with the aid of microorgan¬isms.

Many options are possible here, including yogurt, cheese, pickles, kimchee, bread, sausage, chocolate, etc.

Anaerobic respiration

Molecule other than O2 as terminal electron acceptor Also use modified version of TCA cycle

Aerobic respiration

O2 is terminal electron acceptor

What three general products of the central metabolic pathways does a cell require to carry out biosynthesis?

Precursor metabolites, ATP, and reducing power (in the form of NADPH)

pentose phosphate pathway

Primary role is production precursor metabolites like Ribose 5-phosphate, erythrose 4-phosphate, NADPH, Also breaks down glucose, takes place in the mitochondria in eukaryotes

Catabolism

Processes that degrade compounds to release energy Cells capture to make ATP

flavoproteins

Proteins to which a flavin is attached FAD, other flavins synthesized from riboflavin

(ATP) Oxidative phosphorylation

Proton motive force drives

What is the end product of glycolysis? a) Glucose b) Citrate c) Oxaloacetate d) α-Ketoglutarate e) Pyruvate

Pyruvate

Components of an Electron Transport Chain

Quinones,Cytochromes, and Flavoproteins

How do cells regulate enzyme activity?

Regulated enzymes are allosteric; when a molecule binds to the allosteric site, the enzyme changes shape, with alters its activity.

Enzyme Inhibition

Site to which inhibitor binds determines type

glycolysis

Splits glucose (6C) to two pyruvates (3C) Generates modest ATP, reducing power, precursors

three processes to generate ATP

Substrate-level phosphorylation, Oxidative phosphorylation, and Photophosphorylation

(ATP) Photophosphorylation

Sunlight used to create proton motive force to drive

metabolism

Synthesize new parts Cell walls, membranes, ribosomes, nucleic acids & Harvest energy to power reactions Sum total of these is called metabolism

Which central metabolic pathway generates the most reducing power?

TCA cycle

Which of these pathways gives a cell the potential to produce the most ATP? a) TCA cycle b) Pentose phosphate pathway c) Lactic acid fermentation d) Glycolysis

TCA cycle

Energy is required to reverse the flow of the electron transport chain. Why would this be so?

The "normal" flow of the electron transport chain releases energy so it makes sense that the reverse would require energy. Reversing the electron transport chain takes electrons from a low-energy substance and transfers them to a higher-energy substance electron.

What is the role of transamination in amino acid biosynthesis?

The amino group is removed from one amino acid and donated to another, generating a different amino acid.

Chemolithotrophs near hydrothermal vents support a variety of other life-forms there. Explain how their role is analogous to that of photosynthetic organisms in terrestrial environments.

The chemolithotrophs oxidize the reduced inorganic compounds that spew from the vents, using the energy to fuel CO2 fixation. The organic compounds they then produce can be used as an energy source by chemoorganotrophs in the vent community.

Why are the central metabolic pathways called amphibolic?

They are used in both catabolism and anabolism (amphi means "both kinds").

A student argued that aerobic and anaerobic respiration should produce the same amount of ATP. He reasoned that they both use basically the same process; only the terminal electron acceptor is different. What is the primary error in this student's argument?

The nature of the electron acceptor will make a major difference in the amount of energy produced. A compound such as nitrate has a lower affinity for electrons than oxygen. As a consequence, electron can "fall further" before being accepted by O2 and be used to generate more energy in the form of ATP.

What is the advantage of having tandem photosystems?

The tandem photosystems can raise the energy level of electrons stripped from water to a high enough level that they can be used to generate ATP.

Explain the process used to degrade fatty acids.

They are degraded using β-oxidation, which transfers 2 carbon units from the end of the fatty acid to coenzyme A, forming acetyl-CoA.

Describe the roles of hydrogen sulfide and carbon dioxide in chemolithoautotrophic metabolism.

They are energy sources; prokaryotes oxidize them to harvest energy.

Unlike the cyanobacteria, the anoxygenic photosynthetic bacteria do not produce O2. Why not?

They do not strip electrons from water.

Why would a cell ferment rather than respire?

They ferment if a suitable inorganic terminal electron acceptor is not available, or if they lack an electron transport chain.

Explain how precursor molecules serve as junctions between cata¬bolic and anabolic pathways.

They have two potential fates - they can be broken down to release energy, or they can serve as the carbon skeleton for biosynthesis.

How do enzymes catalyze chemical reactions?

They hold substrates in a way that lowers the activation energy of a specific reaction.

How do the methyl-red and Voges-Proskauer tests differentiate between certain members of the Enterobacteriaceae?

They test for fermentation end products, allowing members of the Enterobacteriaceae that use the 2,3 butanediol pathway to be distinguished from those that use the mixed acid pathway.

In fermentation, the terminal electron acceptor is a) oxygen (O2). b) hydrogen (H2). c) carbon dioxide (CO2). d) an organic compound.

an organic compound

Enzymes

are biological catalysts Name reflects function; ends in -ase Has active site to which substrate binds weakly Causes enzyme shape to change slightly Existing substrate bonds destabilized, new ones form Enzymes are highly specific Enzyme not used up Enzymes are proteins

Precursor metabolites

are intermediates of catabolism that can be used in anabolism, serve as carbon skeletons for building macromolecules

Coenzymes

are organic cofactors Include electron carriers FAD, NAD+, NADP+

Cofactors

assist some enzymes, can assist different enzymes; fewer types needed,include magnesium, zinc, copper, other trace elements

Non-competitive inhibitor

binds to a different site,E.g., mercury oxidizes the S—H groups of amino acid cysteine, converts to cystine Cystine cannot form important disulfide bond (S—S) Enzyme changes shape, becomes nonfunctional

Competitive inhibitor

binds to active site of enzyme Chemical structure usually similar to substrate Concentration dependent; blocks substrate Example is sulfa drugs blocking folic acid synthesis

Electron transport

generates proton motive force that is harvested to make ATP via oxidative phosphorylation.Release coupled to ejection of protons,Prokaryotes: in cytoplasmic membrane.Eukaryotes: in inner mitochondrial membrane Energy gradually released

Three central metabolic pathways in catabolism

glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle

The major pathway(s) of central metabolism are a) glycolysis and the TCA cycle only. b) glycolysis, the TCA cycle, and the pentose phosphate pathway. c) glycolysis only. d) glycolysis and the pentose phosphate pathway only. e) the TCA cycle only.

glycolysis, the TCA cycle, and the pentose phosphate pathway.

Which of these factors does not affect enzyme activity? a) Temperature b) Inhibitors c) Coenzymes d) Humidity e) pH

humidity

role of ATP

is energy currency Composed of ribose, adenine, three phosphate groups Adenosine diphospate (ADP) acceptor of free energy Cells produce ATP by adding Pi to ADP using energy Release energy from ATP to yield ADP and Pi

Substance that loses electrons

is oxidized

Substance that gains electrons

is reduced

Chemoorganotrophs

obtain energy from organic compounds