Micro chapter 11 questions

Major function of TCA cycle?

Glucose (pyruvate) to carbon dioxide.

Why is acetyl CoA energy rich?

Hydrolysis of the bond that links acetic acid to coenzyme A has a large negative change in free energy like the bond in many phosphate-containing molecules.

Protease

Hydrolyze proteins into amino acids which are transported into the cell and catabolized.

Why is aerobic respiration useful?

It allows ATP synthesis by electron transport and oxidative phosphorylation in the absence of O2.

Why is it desirable for a microbe with the Embden-Meyerhof pathway and the TCA cycle also to have the pentose phosphate pathway?

It is advantageous for the cell to carry the pentose phosphate pathway because it is a major producer of NADPH, which is important for its reducing properties. NADPH also protects the cell from reactive oxygen species. 12 NADPH molecules can be generated from 1 glucose molecule in the pentose phosphate pathway.

Photosystem 2

Traps light at shorter wavelengths and transfers its energy to the reaction center, p800.

Hydrogen-oxidizing bacteria:

Many bacteria and archaea can oxidize hydrogen gas using a hydrogenase enzyme. If NADH is produced it can be used in ATP synthesis by electron transport and oxidative phosphorylation.

How do chemolithtrophs obtain ATP & NAD(P)H? What is their most common source of carbon?

Microbes that donate electrons to their ETCs by oxidizing inorganic molecules rather than organic nutrients. The acceptor is usually O2. CO2 is often the carbon source.

Less energy for oxidation is caused by

More positive reduction potentials.

Most common fermentation

Most common fermentation is lactic acid and the reduction of pyruvate to lactate.

What are amphibolic pathways and why are they important?

Pathways with enzymes that function both catholically and anabolically. For instance, many of the enzymes of the Embden-Meyerhof pathway are freely reversible (function catholically during glycolysis by anabolic ally during gluconeogenesis).

Photolithoautotrophy and chemolithoautotrophy:

Photo: use light energy and have CO2 for carbon source. Some use water as the electron source.

Ways organisms are classified based on their requirements for energy, carbon, and electrons.

Phototrophs use light energy. Chemotrophs obtain energy from oxidation of chemical compounds. Lithotrophs use reduced inorganic substances as their electron source. Organotrophs extract electrons from reduced organic compounds . Autotrophs use carbon dioxide. Heterotrophs use reduced organic molecules as their carbon source.

denitrification

Process by which bacteria convert nitrates into nitrogen gas.

Products of the TCA cycle?

(2) CO2 (3) NADH (1) FADH2 (1) ATP or GTP

Process of anaerobic respiration. Does anaerobic respiration yield as much ATP as aerobic respiration?

***Anaerobic respiration produces less ATP than aerobic respiration due to the fact that alternate electron acceptors such as NO3- have less positive reduction potentials than O2. Less energy is available to make ATP in anaerobic because energy yield is directly related to the magnitude of the reduction potential difference. Anaerobic respiration is a chemorganotrophic process where an exogenous terminal electron acceptor (other than O2) is used for electron transport. Mostly done by bacteria/archaea. Produces H2O. Anaerobic electron acceptor is NO3- and produces NO2-. -If oxygen is present, many microbes that carry out anaerobic respiration will perform aerobic respiration.

Difference between nitrification and denitrification:

-Nitrification is a chemolithotropic process that oxidizes ammonia to yield nitrate. -Denitrification is a form of anaerobic respiration that involves oxidizing an organic compound under anoxic conditions.

What are fermentations are why are they useful to many microorganisms?

1) NADH is oxidized to NAD+. 2) O2 is not needed. 3) The electron acceptor is pyruvate or a derivative. 4) An ETC is not used to reoxidize NADH which reduces the ATP yield a lot.

Three major products generated by the fueling reactions. How are they used in anabolic processes?

1. ATP: Primary molecule used to conserve the energy supplied by an energy source. 2. Reducing power: molecules that serve as a ready supply of electrons for chemical reactions. 3. Precursor metabolites: small organic molecules that provide the carbon skeletons needed for biosynthesis of monomers. Photoautotrophs and chemolithoautotrophs are the main producers in ecosystems. They fix CO2 making reduced organic molecules.

1. Current model of oxidative phosphorylation. 2. Structure of ATP synthase:

1. Chemiosmotic hypothesis:Mitochondrial ETCs are organized so that protons move across the inner membrane from the mitochondrial matrix to the inter membrane space as electrons are transported down the chain. 2. ATP synthase is on the inner surface of the palms membrane in bacterial cells. The best studied ATP synthase are the F1F0 found in mitochondria, chloroplasts, and bacteria. They can catalyze ATP hydrolysis. F1 component is spherical attached to the mito. inner membrane surface by a stalk. F0 is embedded in the membrane. F0 (proton movement). F1 is spherical because of alternating a and B subunits; active sites are on B.

Glycolysis (pathways): glucose into pyruvate

1. Embden-Meyerhof 2. Entner-Doudoroff 3. Pentose phosphate pathways

Glycolytic pathways (glycolysis)

1. Embden-Meyerhof: 2. Entner-Doudoroff: 3. Pentose phosphate pathways:

Deamination

1st step in amino acid catabolism; the removal of the amino group from an amino acid.

Photosystem 1

Absorbs longer wavelengths of light and funnels the energy to a reaction center chlorophyll a pair called p700 (absorbs light at 700nm).

Substrate and products of the TCA cycle:

Acetyl CoA---> citrate Citrate---> isocitrate Isocitrate---> a-ketoglutarate + succinylcholine CoA Total= gained (2) NADH; lost (2) carbons Succinyl CoA---> succinate (1) FADH2 + (1) NADH yielded

What chemical intermediate links pyruvate to the TCA cycle?

Acetyl-CoA (pyruvate, end product of glycolysis) but must be decarboxylated and rearranged. NAD+ is reduced to NADH.

What is the difference between aerobic respiration and anaerobic?

Aerobic respiration takes place in the mitochondria and requires oxygen and glucose, and produces carbon dioxide, water, and energy. This process requires oxygen and therefore following anaerobic respiration there is oxygen debt in the cell, as oxygen is needed to break down the lactic acid produced.

What is the difference between aerobic respiration and anaerobic?

Aerobic: process that can totally catabolize a reduced organic energy source to CO2 using the glycolytic pathways and TCA cycle with O2 as the terminal electron acceptor for an electron transport chain Anaerobic glycolysis does not require oxygen and uses the energy contained in glucose for the formation of ATP. This pathway occurs within the cytoplasm and breaks glucose down into a simpler component called pyruvate

Nitrifying bacteria:

Among chemolithotrophs, nitrifying bacteria are soil and aquatic bacteria that carry out nitrification- the oxidation of ammonia to nitrate. Two steps: 1) Ammonia is oxidized to nitrite. 2) The nitrite is oxidized to nitrate.

How do the electron acceptors used in fermentation differ from terminal electron acceptors used during aerobic and anaerobic respiration?

Anaerobic respiration is less energy yielding.

dissimilatory nitrate reduction

Anaerobic respiration using nitrate as the terminal electron acceptor.

Sulfur-oxidizing bacteria:

Bacteria that oxidize suffer to sulfuric acid. Very important ecologically. *They generate ATP by oxidative phosphorylation AND substrate-level phosphorylation.

In what eukaryotic organelle is the TCA cycle found and in bacteria and archaea?

Bacteria/archaea: cytoplasm. Eukaryotes: mitochondrial matrix. -Usually in free-living protists and fungi.

Structure of ETCs and their role in ATP formation. How do mitochondrial chains differ from bacterial and archaea chains?

Bacterial and archaea ETCs can be composed of different electron carriers, employ different terminal oxidases (enter/leave different oxidases), and be branched. Euk. mitochondria: ETC carrier reside in the inner membrane. Bacteria/archaea: ETCs are located within the plasma membrane. Some gram-negative bacteria have ETC carriers in the periplasmic space and our membrane. Shorter than eukaryotes, resulting in the release of less energy,

Chemoorganotrophs

Chemoorganotrophic microorganisms can use three kinds of electron acceptor during energy metabolism. Electrons from the oxidized nutrient can be accepted by an endogenous electron acceptor (fermentation) bu oxygen (aerobic respiration) or by another external electron acceptor (anaerobic respiration).

Electron Transport Chain (ETC)

Composed of a series of electron carriers that operate together to transfer electrons from donors (NADH & FADH2) into O2. Electrons flow from negative to positive reduction potentials. Combine with O2 and H+ to form water.

Why use both photosystems are that same time or just photosystem 1?

Dark reactions of oxygenic phototrophs use three ATP and two NADPH to reduce 1 CO2 to carbohydrate.

Reverse electron flow: how do chemolithotrophs make NAD(P)H?

During reverse electron flow, electrons derived from oxidation of inorganic substrates (reduced nitrogen or sulfur compounds) are moved up their ETCs to reduce NAD(P)+ to NAD(P)H. This is not thermodynamically favorable so energy in the form of PMF must be used to push electrons from molecules of positive reduction potentials to those that are more negative.

End product of glycolysis?

Pyruvate

Types of electron acceptors used by fermentation and respiration:

Reduced electron carriers (NADH, FADH2, NAD+) in turn donate the electrons to an electron transport chain; the metabolic process called respiration. Aerobic respiration: final electron acceptor is oxygen. Anaerobic respiration: terminal acceptor is an oxidized molecule such as NO3-, SO4 2-, CO2, Fe3+. Fermentation: uses an electron acceptor that is endogenous (within cell) and does not involve the electron transport chain. ATP is synthesized, in fermentation by substrate-level phosphorylation.

Substrate level phosphorylation

Small amount of ATP made in this process. Most organisms synthesize ATP only by substrate-level phosphorylation. During fermentation, ATP is synthesized almost exclusively by substrate-level phosphorylation: process in which a phosphate is transferred to ADP from a high energy molecule generated by catabolism of the energy source.

P/O value

The amount of ATP synthesized as the result of the oxidation of NADH. About 10 protons move across the membrane due to NADH oxidation.

Why is it to the cells advantage to catabolize diverse organic energy sources by funneling them into a few common pathways?

The existence of a few metabolic pathways that each degrade many nutrients greatly increases metabolic efficiency by avoiding the need for a large number of less metabolically flexible pathways. Some pathways funnel metabolites into the glycolytic pathways and the tricarboxylic acid cycle, thus increasing efficiency and flexibility.

Photophosphorylation

The production of ATP by chemiosmosis during the light reactions of photosynthesis.

How do substrate-level phosphorylation and oxidative phosphorylation differ?

Two ATPs are generated by substrate-level phosphorylation per glucose converted into pyruvate. It takes two turns of the TCA cycle to generate the two ATP per glucose. Oxidative phosphorylation synthesizes ATP as a result of electron transport driven by the oxidation of a chemical energy source. Most of the ATP made during aerobic respiration is generated by oxidative phosphorylation. *Oxidative phosphorylation accounts for 7X more ATP than substrate-level.

Autotrophs

Use CO2 as their carbon source.

Heterotrophs

Use reduced organic molecules as their carbon source.

Homolactic fermenters

Use the Embden-Meyerhof pathway.

Heterolactic fermenters

Use the pentose pathway.

Transamination

Used for degradation of amino acids, takes the amino group to a ce-keto acid acceptor. Accomplishes deamination: 1st step in amino acid catabolism; the removal of the amino group from an amino acid.

Oxidative phosphorylation

Used to synthesize most of the cellular ATP.