Microbiology Chapter 8: Microbial Metabolism

chemo-

-"chemical"

Pyrophosphate

-when these high-energy bonds are broken to release two connected phosphate groups from ATP

Anaerobic respiration

-using an inorganic molecule other than oxygen as final electron acceptor

Adenosine Triphosphate (ATP)

-"energy currency" of the cell -versatile compound can be used to fill any energy need of the cell

photo-

-"light"

hetero-

-"other"

auto-

-"self"

Lithotrops

-("litho" means "rock") are chemotrophs that get energy from inorganic compounds, including hydrogen sulfide (H2S) and reduced iron

Chemoautotrophs

-Chemotroph -Energy Source: chemical -Carbon Source: inorganic -Examples: Hydrogen-, sulfur-, iron-, nitrogen-, and carbon monoxide-oxidizing bacteria

Chemoheterotrophs

-Chemotrophs -Energy Source: chemical -Carbon Source: organic compound -Examples: all animals, most fungi, protozoa, and bacteria

Anabolic Reactions (anabolism)

-Endergonic reactions involved in biosynthesis of simple molecules into complex ones -refers to those endergonic metabolic pathways involved in biosynthesis, converting simple molecular building blocks into more complex molecules, and fueled by the use of cellular energy.

What are some alternatives to glycolysis?

-Entner-Doudoroff (ED) Pathway -Pentose phosphate pathway

Substrate Concentration influences on Enzymes

-Enzymes activity is increased at higher concentrations of substrate until it reaches a saturation point at which then enzyme can bind no additional substrate -overall, enzymes are optimized to work best under the environmental conditions in which the organisms that produce them live.

pH influence on Enzymes

-Enzymes are also suited to function best within a certain pH range, and, as with temperature, extreme environmental pH values (acidic or basic) can cause enzymes to denature -Active-site amino-acid side chains have their own acidic or basic properties that are optimal for catalysis and, therefore, are sensitive to changes in pH.

What can Enzyme inhibitors regulate?

-Enzymes can be regulated in ways that either promote or reduce their activity.

Catabolic reactions (catabolism)

-Exergonic reactions that break down complex molecules into simpler ones

Photoheterotrophs

-Phototrophs -Energy Source: light -Carbon Source: organic compounds -Examples: green and purple non sulfur bacteria, heliobacteria

Photoautotrophs

-Phototrops -Energy Source: light -Carbon Source: inorganic -Examples: all plants, algae, cyanobacteria, and green and purple sulfur bacteria

Substrate-level phosphorylation

-a phosphate group is removed from an organic molecule and is directly transferred to an available ADP molecule, producing ATP.

Catalyst

-a substance that helps speed up a chemical reactions -they are not used or changed during chemical reactions and, therefore are reusable

Reduction Reactions:

-add electrons to acceptor molecules leaving them reduced

Metabolism

-all of the chemical reactions inside of a cells

Pentose Phosphate Pathway (PPP)

-alternative pathway to glycolytic pathway that produces intermediates used for the biosynthesis of nucleotides and amino acids -it generates NADPH and pentoses as well as ribose 5-phosphate, precursor for the synthesis of nucleotides -also called the phosphogluconate pathway or the hexose monophosphate shunt

Entner-Doudoroff (ED) pathway

-alternative pathway used for some bacteria -Another pathway to go from glucose to pyruvate - Similar to glycolysis, but yields less energy -variant of the glycolytic pathway that produces 1 ATP per glucose and acids

Temperature influence on Enzymes

-although increasing the environmental temperature generally increases reaction rates, enzyme catalyzed or otherwise, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site, making them less well suited bind substrates.

Several of the intermediate compounds in the Krebs cycle can be used in synthesizing a wide variety of important cellular molecules, including...

-amino acids, chlorophylls, fatty acids, and nucleotides -therefore, the cycle is both anabolic and catabolic.

The energy of the electrons is harvested to generate...

-an electrochemical gradient across the membrane, which is used to make ATP by oxidative phosphorylation

Cofactor

-are inorganic ions such as iron (Fe2+) and magnesium (Mg2+) that help stabilize enzyme conformation and function -Example: of an enzyme that requires a metal ion as a cofactor is the enzyme that builds DNA molecules, DNA polymerase, which requires a bound zinc ion (Zn2+) to function.

Coenzyme

-are organic helper molecules that are required for enzyme action. -like enzymes, they are not consumed and, hence, are reusable. -the most common sources of coenzymes are dietary vitamins, which some vitamins are precursors to coenzymes and others act directly as coenzymes.

Redox Reactions

-because electrons can move from one molecule to another, Oxidation and Reduction reactions occur together in tandem

Cellular Respiration

-begins when electrons are transferred from NADH and FADH2--- made in glycolysis, the transition reaction, and the Krebs cycle--- through a series of chemical reactions to final inorganic electron acceptor (either oxygen in aerobic respiration or non-oxygen inorganic molecules in anaerobic respiration).

Noncompetitive (allosteric) inhibitor

-binds to the enzyme at an allosteric site, a location over than the active site, and still manages to block substrate binding to the active site by inducing a conformational change that reduces the affinity of the enzyme for its substrate.

Glycolysis produces pyruvate, which...

-can be further oxidized to capture more energy

Metabolic Pathways

-cellular processes such as the building or breaking down of complex molecules occur through series of stepwise, interconnected chemical reactions

The Krebs cycle is a...

-closed loop -the last part of the pathway regenerates the compound used in the first step -the eight steps of the cycle are a series of chemical reactions that capture the two-carbon acetyl group (the CoA carrier does not enter the Krebs cycle) from the transition reaction, which is added to a four-carbon intermediate in the Krebs cycle, producing the six-carbon intermediate citric acid (giving the alternate name for this cycle). -as one turn of the cycle returns to the starting point of the four-carbon intermediate, the cycle produces two CO2 molecules, one ATP molecule (or an equivalent, such as guanosine triphosphate (GTP)) produced by substrate-level phosphorylation, and three molecules of NADH and one of FADH2.

What are the four major classes of electron carriers involved in both eukaryotic and prokaryotic electron transport systems are the...

-cytochromes -flavoproetins -iron-sulfur proteins -quinones

Cytochrome oxidase

-electron carrier -differences between bacterial types and can be used to differentiate closely related bacteria for diagnoses.

Transition Reaction

-electrons are also transferred to NAD+ to form NADH -to proceed to the next phase of this metabolic process, the comparatively tiny two-carbon acetyl must be attached to a very large carrier compound called coenzyme A (CoA). -this occurs in the mitochondrial matrix of eukaryotes -in prokaryotes, it occurs in the cytoplasm because prokaryotes lack membrane-enclosed organelles.

Dephosphorylation

-energy is released to drive endergonic reactions

What is an important mechanism of allosteric regulation in cells?

-feedback inhibition, where the end product of the pathway serves as a noncompetitive inhibitor to an enzyme early in the pathway.

Bridge Reaction (also called Transition Reaction)

-for pyruvate to enter the next oxidative pathway, it must first be decarboxylated by the enzyme complex pyruvate dehydrogenase to a two-carbon acetyl group

Phototrophs

-get their energy for electron transfer from light

Inorganic phosphate

-when these high-energy bonds are broken to release one phosphate from ATP

What will high temperatures do to enzymes?

-high temperatures will eventually cause enzymes, like other biological molecules, to denature, losing their three-dimensional structure and function.

During glycolysis...

-high-energy phosphate groups from the intermediate are added to ADP to make ATP

Organotrophs

-including humans, fungi, and many prokaryotes, are chemotrophs that obtain energy from organic compounds

Although some bacteria...

-including the opportunistic gram-negative pathogen Pseudomonas aeruginosa, contain only the ED pathway for glycolysis, other bacteria, like E. coli, have the ability to use either the ED pathways or the EMP pathway.

The Krebs cycle, also known as the citric acid cycle, is summarized as...

-incoming two-carbon acetyl results in the main outputs per turn of two CO2, three NADH, one FADH2, and one ATP (or GTP) molecules made by substrate-level phosphorylation.-two turns of the Krebs cycle are required to process all of the carbon from one glucose molecule.

Feedback Inhibition

-involves the use of a pathway product to regulate its own further production.

Ribose

-is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA

Competitive Inhibitor

-is a molecule similar enough to a substrate that it can compete with the substrate for binding to the active site by simply blocking the substrate from binding

Holoenzyme

-is active -an enzyme with the necessary associated cofactor or coenzyme

Adenosine monophosphate (AMP)

-is composed of an adenine molecule bonded to a ribose molecule and a single phosphate group -is at the heart of ATP

Apoenzyme

-is inactive -an enzyme lacking a necessary cofactor or coenzyme

Adenosine Diphosphate (ADP)

-is the addition of a second phosphate group to this core molecule results in this formation

Glycolysis

-is the most common pathway for the catabolism of glucose

Electron Transport System (ETS)

-it comprises a series of membrane-associated protein complexes and associated mobile accessory electron carries -it is a series of chemical reactions that resembles a bucket brigade in that electrons from NADH and FADH2 are passed rapidly from one ETS electron carrier to the next. -These carriers can pass electrons along in the ETS because of their redox potential.

For a protein or chemical to accept electrons...

-it must have a more positive redox potential than the electron donor. -Therefore, electrons move from electron carriers with more negative redox potential of those with more positive redox potential

Catabolism

-large molecules are broken down into smaller ones, releasing energy

Pentose-Phosphate Pathway is a...

-metabolic pathway parallel to glycolysis that generates NADPH and five-carbon sugars as well as ribose 5-phosphate, a precursor for the synthesis of nucleotides from glucose.

Entner-Doudoroff Pathway is a...

-metabolic pathway that converts glucose to ethanol and nets one ATP

Electron Carriers

-molecules that bind to and shuttle high-energy electrons between compounds in pathways

Entner-Doudoroff (ED) pathway Name

-named after its discoverers Nathan Entner and Michael Doudoroff (1911-1975)

The principal electron carriers we will consider originate from the B vitamin group and are derivatives of nucleotides:

-nicotinamide adenine dinucleotide -nicotine adenine dinucleotide phosphate -flavin adenine dinucleotide

The Pentose Phosphate Pathway may be favored when the cell has the need for...

-nucleic acid and/or protein synthesis, respectively.

Chemotrophs

-obtain energy for electron transfer by breaking chemical bonds

Where does the Krebs cycle occur?

-occurs in the cytoplasm of prokaryotes along with glycolysis and the transition reaction, but it takes place in the mitochondrial matrix of eukaryotic cells where the transition reaction also occurs

Where do electron transfers take place?

-on the inner part of the cell membrane of prokaryotic cells or in specialized protein complexes in the inner membrane of the mitochondria of eukaryotic cells

How many inhibitor molecules are needed per enzyme for effective inhibition?

-only one inhibitor molecule is needed per enzyme for effective inhibition, the concentration of inhibitors needed for noncompetitive inhibition is typically much lower than the substrate concentration.

Autotrophs

-organisms that convert inorganic carbon dioxide (CO2) into organic carbon compounds

What are the two types of Chemotrophs?

-organotrophs -lithotrophs

What are Enzymes subject to influences by local environmental conditions such as...

-pH -substrate concentration -temperature

Exergonic Reactions

-reactions which relate energy -reactions that are spontaneous

Endergonic Reactions

-reactions which require energy to proceed

Binding of an allosteric inhibitor _______________ enzyme activity, but binding of an allosteric activator _________________ enzyme activity.

-reduces; increases

Heterotrophs

-rely on more complex organic carbon compounds as nutrients -these are provided to them initially by autotrophs

Oxidation Reactions

-removes electrons from a donor molecule leaving them oxidized

Phosphorylation

-requires energy -adding a phosphate group to a molecule

Glycolysis begins with...

-single six-carbon glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate.

Anabolism

-small molecules are assembled into larger ones, using energy

Microbes using anaerobic respiration commonly have an intact Krebs cycle,...

-so these organism can access the energy of NADH and FADH2 molecules formed -Howeve, anaerobic respires use altered ETS carriers encoded by their genomes, including distinct complexes for electron transfer to their final electron acceptors -small electrochemical gradients are generated from these electron transfer systems, so less ATP is formed through anaerobic respiration

Examples of Metabolism

-start with the catabolism of polysaccharides such as glycogen, starch, or cellulose -Enzymes such as amylase, which breaks down glycogen or starch, and cellulases, which break down cellulose, can cause the hydrolysis of glycosidic bonds between the glucose monomers in these polymers, releasing glucose for further catabolism.

Where does glycolysis take place?

-takes place in the cytoplasm of prokaryotic and eukaryotic cells.

Allosteric Activators

-that bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme's active site(s) for its substrate(s).

Induced Fit

-the active-site modification int he presence of substrate, along with the simultaneous formation of the transition state

High-energy phosphate bonds

-the bonds between phosphate groups are unstable (one in ADP and two in ATP)

There are many circumstances under which aerobic respiration is not possible, including any one or more of the following:

-the cell lacks genes encoding an appropriate cytochrome oxidase for transferring electrons to oxygen at the end of the electron transport system -the cell lacks genes encoding enzymes to minimize the severely damaging effects of dangerous oxygen radicals produced during aerobic respiration, such as hydrogen peroxide (H2O2) or superoxide (O2-) -the cell lacks a sufficient amount of oxygen to carry out aerobic respiration

Substrates

-the chemical reactants to which an enzyme binds

Activation Energy

-the energy needed to form or break chemical bonds and convert reactants to products

What is needed for a competitive inhibitor to be effective?

-the inhibitor concentration needs to be approximately equal to the substrate concentration

Active sites

-the location within the enzyme where the substrate binds in the enzyme

Aerobic Respiration

-the one having the most positive redox potential -the final electron acceptor at the end of the ETS is an oxygen molecule (O2) that becomes reduced to water (H2O) by the final ETS carrier

Chemiosmosis

-the potential energy of this electrochemical gradient generated by the ETS causes the H+ to diffuse across a membrane (the plasma membrane in prokaryotic cells and the inner membrane in mitochondria in eukaryotic cells). -this flow of hydrogen ions across the membrane, must occur through a channel in the membrane via a membrane-bound enzyme complex

Biosynthesis

-the production of complex molecules within living organisms or cells

Krebs Cycle

-transfers remaining electrons from the acetyl group produced during the transition reaction to electron carrier molecules, thus reducing them.

Overall, in this process of glycolysis, the net gain from the breakdown of a single glucose molecule is:

-two ATP molecules -two NADH molecule -two pyruvate molecules

Emben-Meyerhof-Parnas Pathways (EMP) Parts

-used by animals and many bacteria Part 1: is called the energy investment phase, uses energy from two ATP molecules to modify a glucose molecule so that the six-carbon sugar molecule can be spilt evenly into two phophorylated three-carbon molecules called glyceraldehyde 3-phosphate (G3P) Part 2: is called the energy payoff phase, extracts energy to oxidizing G3P to pyruvate, producing four ATP molecules reducing two molecules of NAD+ to two molecules of NADH, using electrons that originated from glucose.

Enzymes

-whereas inorganic molecules may serve as catalysts for a wide range of chemical reactions, proteins, that serve as catalysts for biochemical reactions inside cells -they play an important role in controlling cellular metabolism -an enzyme functions by lowering the activation energy of a chemical reaction inside the cell

In Glycolysis, for each glucose...

-you end up with 2 pyruvate molecules, 2 NADH electron carrier molecules, and a net gain of 2 ATP

What is the process of forming an Active Holoenzyme?

1. Aponenzyme becomes active by binding coenzyme or cofactor to enzyme. 2. Holoenzyme is formed when associated cofactor or coenzyme binds to the enzyme's active site.

What are the steps for the Induced-Fit Model?

1. Substrate enters active site of enzyme. 2. Enzyme/substrate complex forms. 3. Substrate is converted to products. 4. Products leave the active site of the enzyme.

Fermentation Products

Pathways: -Acetonebutanol-ethanol -Alcohol -Butanediol -Butyric acid -Lactic acid -Mixed acid -Propionic acid

In Glycolysis, ATP is produced by...

substrate-level phosphorylation