Metabolism: Fueling Cell Growth

Feedback inhibition

End product of a given biosynthetic pathway generally acts as an allosteric inhibitor of the first enzyme of that pathway. (Regulatory molecule is usually end product). Allows product of the pathway to modulate its own synthesis.

Factors that Influence Enzyme activity

Environmental factors influence how well enzymes function and multiply. Enzymes have a narrow range of factors including temperature, pH, and salt concentrations. A 10 C rise in temperature, doubles the speed of enzymatic reactions, until optimal reaction is reached. Proteins will denature at high temperatures and will not function. Most enzymes operate best at low salt concentrations and at pH values slightly above 7.

Polysaccharides and disaccharides

Enzymes called Amylases digest starch and enzymes called cellulases digest cellulose. Disaccharides including lactose, maltose and sucrose are hydrolyzed by specific disaccharidases.

Active site

Enzymes surface or catalytic site, typically a relatively small crevice. This is the critical site to which a substrate binds by weak forces. The binding causes the shape of enzyme to change slightly. Existing substrate bonds destabilized and new ones form. Enzymes are highly specific (hand fits glove) Enzyme not used up, can be reused again and again.

Electron Transport Chain Continued...

Expulsion of protons creates a proton gradient or electrochemical gradient, across the membrane. Energy of this gradient, proton motive force, can be harvested by cells and used to fuel the synthesis of ATP. Prokaryotes can also power transporters using flagella.

Lipids

Fats are hydrolyzed by enzymes called lipases. The glycerol is then converted to a precursor metabolite dihydroxyacetone phosphate, which then enters the glycolytic pathway. Fatty acids are degraded using a reaction called B-oxidation to enter the TCA cycle.

Chemolithotrophs- Four general groups Table 6.7

Hydrogen bacteria Sulfur bacteria Iron bacteria Nitrifying bacteria

Chemiosmotic Theory

In 1961, the British scientist Peter Mitchell originally proposed this theory, which describes the remarkable mechanism by which ATP synthesis is linked to electron transport, but his hypothesis was dismissed until it was valid and won a Nobel Prize in 1978.

Fermentation Continued...

In order for glycolysis to continue they use pyruvate or a derivative as a terminal electron acceptor by transferring the electrons carried by NADH to pyruvate or a derivative, NAD+ is generated so it can once again accept electrons in the steps of glycolysis.

Photosynthesis

Plants, algae, several groups of bacteria Converting sunlight energy into chemical energy. General reaction is 6 CO2 + 12 H2X --------> C6H12O6 + 12X + 6H2O where X indicates element such as oxygen or sulfur Process can be distinct into two stages- light-dependent and light independent reactions.

Photosynthetic

organisms harvest the energy of sunlight, using it to power the synthesis of organic compounds such as glucose. Power synthesis of organic compounds from CO2. Convert kinetic energy of photons to potential energy of chemical bonds

Endergonic

products have more free energy than reactants, the reaction requires an input of energy.Change in free energy is same regardless of number of steps involved (e.g., converting glucose to CO2 + H2O) Cells use multiple steps when degrading compounds.Energy released from exergonic reactions powers endergonic reactions

Chemolithotrophs

prokaryotes as a group are unique in their ability to use reduced inorganic chemicals such as hydrogen sulfide (H2S) and ammonia (NH3) as a source of energy. These compounds produce by anaerobic respiration when inorganic molecules such as sulfate and nitrate serve as terminal electron acceptors. Results in important example of nutrient cycling.

Exergonic

reactants have more free energy. Energy is released in reaction

Lipid synthesis

requires fatty acid and glycerol synthesis. Starts with transfer f acetyl group of the acetyl-CoA to acyl carrier protein (ACP). This carrier holds fatty acid chain as 2- carbon units are added. The glycerol component of fat is synthesized from dihydroxyacetone phosphate which is generated in glycolysis.

Potential Energy

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

Nucleotide synthesis

subunits of DNA and RNA are synthesized as ribonucleotides. Purines: atoms added to ribose 5-phosphate to form ring Pyrimidines: ring made, then attached to ribose 5-phosphate Can be converted to other nucleobases of same type

Central metabolic pathways

three key metabolic pathways that are used to gradually oxidize glucose, the preferred energy source of many cells, completely to carbon dioxide. They include -Glycolysis -Pentose phosphate pathways -Tricarboxylic acid cycle.

Hydrolytic Enzymes

to break down the polysaccharides, lipids and proteins to their subunits they use this enzymes which break bonds by adding water. They are subunits transported into the cell where are further degraded to form appropriate precursor metabolites.

Respiration

transfers electrons from glucose to electron transport chain. Electron transport chain generates proton motive force. Harvested to make ATP via oxidative phosphorylation

Light-independent Reactions (dark reactions)

use the energy to synthesize organic compounds. The process that converts carbon dioxide into organic compounds are called carbon fixation.

Light-dependent Reaction (light reactions)

use to capture the energy from light and convert it to chemical energy in the form of ATP

Free energy

amount of energy available for harvest by breaking down a compound. (available to work). energy is released when chemical bond is broken.

Proteins

are hydrolyzed by enzymes called proteases, which break peptide bonds that join amino acid subunits. Amino group of the amino acids is removed by a reaction called a deamination. Remaining carbon skeletons are then converted into appropriate precursor molecules.

Precursor metabolites

are metabolic intermediates produced at specific steps in catabolic pathways that can be used in anabolic pathways. Glucose serves as a energy source. Starting points for all cell components including proteins, carbohydrates, lipids and nucleic acids.

Coenzymes Table 6.4

are organic cofactors that act as loosely bound carriers of molecules or electrons. Include electron carriers FAD, NAD+, NADP+.

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

Transition Step

-CO2 is removedfrom pyruvate -Electrons reduce NAD+ toNADH+ H+ -2-carbon acetyl group joined to coenzyme A to form acetyl-CoA -Takes place in mitochondria in eukaryotes

Microbes can use variety of compounds (cont...)

-Convert to precursor metabolites -Enter appropriate metabolic pathways

Central metabolic pathways continued...

-Key outcomes ATP Reducing power Precursor metabolites

Aerobic respiration

...

Sulfate-reducers (Electron Transport Chain of Prokaryotes)

A group of obligate anaerobes use sulfate (SO4 2-) as a terminal electron acceptor, producing hydrogen sulfide as an end product.

Hydrogenation

A reduction reaction in which an electron and an accompanying proton are added .

Role of ATP

Adenosine triphospate (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

Metabolic Pathways Continued...

An Electron-proton pair, or hydrogen atom is often removed Substance that loses electrons is oxidized (removal of hydrogen atom) Substance that gains electrons is reduced ( addition of a hydrogen atom)

Role of Enzymes

An enzyme facilitates each step of a metabolic pathway. Enzymes are proteins that function as biological catalysts, accelerating the conversion of one substance, the substrate, into another, the product by lowing activation energy. Without enzymes, energy-yielding reactions would still occur, but as a extremely slow rate.

Dehydrogenation

An oxidation reaction in which an electron and an accompanying proton are removed

Enzymes (cont...)

Are proteins that act as biological catalyst, facilitating the conversion of a substrate into a product. Suffix Name reflects function; ends in -ase.

Calculating yields of ATP

Based on experiments on rat mitochondria: ~2.5 ATP made per electron pair from NADH ~1.5 ATP made per electron pair from FADH2

Trycarboxylic Acid (TCA) Cycle

Completes oxidation of glucose -Produces 2 CO2 2 ATP 6 NADH 2 FADH2 Precursor metabolites

Calculating theoretical maximum yields prokaryotes:

In prokaryotes: Glycolysis: 2 NADH 6 ATP Transition step: 2 NADH 6 ATP TCA Cycle: 6 NADH 18 ATP; 2 FADH2 4 ATP Total maximum oxidative phosphorylation yield = 34 ATP

ATP Synthase—Harvesting the Proton Motive

Just as energy is required to create a concentration gradient, energy is released when gradient is at ease. Enzyme ATP synthase uses that energy to synthesize ATP. Permits protons to flow back in cell in a controlled manner, harvesting energy released to fuel addition phosphate group to ADP. 1 ATP formed from entry of ~3 protons

Anaerobic respiration

Less efficient form of energy transformation than aerobic. Due to lesser amount of energy released. Alternative electrons carriers used in electron transport during anaerobic. Uses nitrate as terminal electron acceptor

Organic compounds other than Glucose

Microbes can use a variety of organic compounds other than glucose as energy sources, including macromolecules such as polysaccharides, lipids and proteins.

Continued...

More energy released when difference in electronegativity is greater -Electron donor: Energy source -Acceptor: Terminal electron acceptor

Aerobic respiration

O2 is the terminal electron acceptor, producing water

Products

Or final compounds, energy is released in the reaction.

Photosynthesis Table 6.8 (Oxygenic)

Plants, algae and cyanobacteria

Glycolysis

Primary pathways used by many organisms to convert glucose to pyruvate. 1 molecule of glucose is converted into 2 molecules of pyruvate. This generates a net gain of 2 ATP molecules and 2 NADH molecules.

Anabolic Pathways-Synthesizing Subunits from Precursor Molecules

Prokaryotes are highly diverse but are similar to their biosynthetic processes. They synthesize subunits, employing specific anabolic pathways that use ATP reducing power in for NADPH and the precursor metabolites formed in central metabolic pathways. Organisms lacking enzymes must have the end product from external source. This is why fastidious bacteria require many growth factors.

Metabolic Pathways

Prokaryotes remarkably diverse in using energy sources and terminal electron acceptors. Use organic (glucose) or inorganic(hydrogen sulfide or ammonia) as energy sources. Electrons are removed or transferred through series of oxidation-reduction reactions or redox reactions

Photosynthesis (Anoxygenic)

Purple and green bacteria

Reducing Power

Reduced electron carriers represent reducing power because their bonds contain a form of usable energy. (easily transfer electrons to molecules) Raise energy level of recipient molecule.

Metabolic pathways

Series of chemical reactions (intermediates) that convert starting compound final product or end product. May be linear, branched, cyclical. Sometimes organic weak acids.

Calculating theoretical maximum yields eukaryotic:

Slightly less in eukaryotic cells NADH from glycolysis in cytoplasm transported across mitochondrial membrane to enter electron transport chain Requires ~1 ATP per NADH generated

Role of the Chemical Energy Source and the Terminal Electron Acceptor

Some atoms, molecules more electronegative than other -Greater affinity for electrons -Energy released when electrons move from low affinity molecule to high affinity molecule (E.g., glucose to O2)

General Mechanisms of Proton Ejection

Some carriers accept only hydrogen atoms (proton-electron pairs), others only electrons Spatial arrangement in membrane shuttles protons to outside of membrane. When hydrogen carrier accepts electron from electron carrier, it picks up proton from inside cell or mitochondrial matrix. When hydrogen carrier passes electrons to electron carrier, protons released to outside of cell or intermembrane space of mitochondria. Net effect is movement of protons across membrane. Establishes concentration gradient. Driven by energy released during electron transfer.

Cofactors

Some enzymes act with the assistance of a non-protein component which include magnesium, zinc, copper, other trace elements.

Three processes to generate ATP

Substrate-level phosphorylation- Exergonic reaction power Oxidative phosphorylation- Proton motive force drives same Photophosphorylation- Sunlight used to create proton motive force to drive

ATP Yield of Aerobic Respiration in Prokaryotes

Substrate-level phosphorylation: 2 ATP (from glycolysis; net gain) 2 ATP (from the TCA cycle) 4 ATP (total) Oxidative phosphorylation: 6 ATP (from reducing power gained in glycolysis) 6 ATP (from reducing power gained in transition step) 22 ATP (from reducing power gained in TCA cycle) 34 (total) Total ATP gain (theoretical maximum) = 38

Allosteric Regulation

These enzymes can be controlled because they are allosteric enzymes, which have a binding site called an allosteric site that is separate from their active site. When regulatory binds to the active site, the shape of the enzyme changes.

Electron Carriers

Three type of electron carriers that participate in reactions that oxidize the energy source. They include NAD+, FAD, AND NADP+. In reduced forms they are NADH, FADH2 AND NADPH.

Electron Transport Chain of Prokaryotes

Tremendous variation: even single species can have several alternate carriers. E. coli serves as example of diversity found even in a single organism.

Terminal Electron Acceptor

Ultimately the electrons are transferred to a molecule such as O2 that functions as the terminal electron acceptor.

Pentose Phosphate Pathway

Used by cells to break down glucose. Important in contribution to biosynthesis. The reducing power generates NADPH, which is used in biosynthetic reactions when reduction is required. Important in biosynthesis of precursor metabolites are Ribose 5-phosphate, erythrose 4-phosphate

Respiration

Uses the NADH and FADH2 generated in glycolysis, the transition step, and the TCA cycle to synthesize ATP.

Non-competitive Inhibition

binds to a different site. Allosteric inhibition, is an example of non-competitive reversible inhibition and is used by the cell to modulate its processes. Non competitive, non-reversible inhibitors damage the enzyme permanently so that it can no longer function; the inhibitor acts as an enzyme poison. E.g., mercury oxidizes the S-H groups of amino acid cysteine, converts to cystine. Enzyme changes shape, which becomes nonfunctional.

Enzyme Inhibition

can be inhibited by a variety of compounds other than the regulatory molecules normally used by the cell. Inhibitory compound can be exploited to prevent microbial growth. The site to which the molecule binds too determines whether they function as competitive or non-competitive inhibitors.

Fermentation end products varied

can sometimes held in identification and some end products are commercially valuable. Ethanol, Butyric acid , Propionic acid, 2,3-Butanediol and Mixed acids

Fermentation

cells that cannot respire are limited by their inability to recycle reduced electron carriers. Cell has limited number of carrier molecules and if electrons are not removed from the reduced electrons, then non will be available to accept electrons. As a result glycolysis will stop.

Kinetic Energy

energy of movement (e.g., moving water. Energy in universe can not be created or destroyed, but it can be converted between forms

Anabolism

or biosynthetic, includes processes that utilize energy stored in ATP to synthesize and assemble subunits(building blocks) of macromolecules that make up the cell. These include, amino acids, nucleotides and lipids. Use ATP to drive reactions

Reactants

or starting compounds, have more free energy than products.

Electron Transport

generates proton motive force, and an enzyme called ATP synthase, which harvests the energy of the proton motive force to drive the synthesis of ATP.

Competitive Inhibition

inhibitor binds to the active site of the enzyme, obstructing access of the substrate to that site. This occurs because the inhibitor has a chemical structure similar to the normal substrate. Concentration dependent; blocks substrate. Example of competitive inhibition is the action of sulfanilamide, one of the sulfa drugs as an antimicrobial medication which blocks folic acid synthesis.

Electron Transport Chain

is a group of membrane-embedded electron carriers that pass electrons sequentially from one to another (eject protons in process). In prokaryotes is located in the cytoplasmic membrane. In Eukaryotes is located in the Mitochondria.

Anaerobic respiration

is similar to aerobic but uses other molecules other than O2 as terminal electron acceptor. In addition, modified versions of the TCA cycle that generates less reducing power are used during anaerobic respiration.

Yields of Pentose Phosphate Pathway

it varies, depending on which of several possible alternatives are taken.

Chemoorganotrophs

obtain energy by degrading organic compounds such as glucose, releasing energy of their chemical bonds. Depend on solar energy harvested by photosynthetic organisms (synthesize glucose).

Fermentation

used by organisms that cant respire because inorganic terminal electron is not available or lack an electron transport chain. E. coli is facultative anaerobe Aerobic respiration, anaerobic respiration, and fermentation. Streptococcus pneumoniae lacks electron transport chain; Fermentation only option. ATP-generating reactions are only those of glycolysis Additional steps consume excess reducing power to Regenerate NAD+

Catabolism

uses the energy that is being released during the breakdown of compounds such as glucose, using that energy to synthesize ATP and release energy (the energy currency of all cells). Linked w/ anabolism.

Electron donor

when electrons are removed from the energy source (electron donor) they are temporarily transferred to a specific molecule that serves as an electron carrier.